text:
|By Marketwired .
Article Rating:
|January 31, 2013 09:31 AM EST
GENEVA -- (Marketwire) -- 01/31/13 -- Developers of high-end set-top boxes and video gateways can significantly reduce time to market for their new products offering rich multi-screen viewing experiences, by taking advantage of the Reference Design Kit (RDK) from Comcast, now pre-integrated with the Orly STiH416 system-on-chip from STMicroelectronics (NYSE: STM), a global semiconductor leader serving customers across the spectrum of electronics applications and a leading provider of set-top box ICs.
By pre-integrating the RDK with its STiH416 system-on-chip for advanced HD set-top boxes, ST is enabling its customers to bring new products to market faster by saving software integration time. ST's STiH416, announced in 2011, is the industry's highest performing set-top box IC, and has the unique ability to support gateway, server and client applications.
"Combining the leading performance of our STiH416 with the flexibility and rich features of RDK enables our customers to create new, high-performing products extremely quickly, and allows efficient customization for specific target markets," said Gian Luca Bertino, Executive VP, General Manager, Digital Convergence Group, STMicroelectronics.
The RDK from Comcast is a pre-integrated software bundle that creates a common framework for powering tru2way®, IP or hybrid set-top boxes and gateway devices and accelerates the development and deployment of next-generation video services. Comcast licenses the RDK to OEMs, System Integrators, SoC and software vendors as well as Multichannel Video Programming Distributors to create a community of innovators focused on bringing rich, multi-screen TV home entertainment experiences to consumers faster.
About the STiH416:
ST's STiH416 is the first device of its type to feature the advanced dual-core ARM® Cortex-A9 MPCore application processor. Combined with the ARM® Mali® 3D graphics processor, a dedicated transport processor,and a transcoder for adaptive video streaming, this creates a high-performance multimedia processing subsystem capable of:
- Decoding MVC (Multi-View Coding) 3DTV, H.264/MPEG2/4 and Internet video standards such as DivX, VC1 and Google Webm/VP8, all with outstanding Faroudja video image quality;
- Seamless distribution of HD content from any source to multiple screens in the home, such as TV, PC, mobile or tablet;
- Support for rich on-screen graphics such as advanced user guides and games;
- Management of software environments such as Android, Qt, HTML5, Adobe Flash® Player and Adobe AIR to support next-generation IPTV, Over The Top (OTT) services and apps;
- H.264 video encoder up to 1080p60 HD resolution to enable any client devices in the home.
There is also a dedicated security engine meeting the latest Conditional Access (CA) and Digital Rights Management (DRM) standards. Moreover, with multiple power-management modes and advanced process technology, the STiH416 is optimized for very low power consumption -- less than 30mW in standby mode.
About STMicroelectronics
ST is a global leader in the semiconductor market serving customers across the spectrum of sense and power and automotive products and embedded processing solutions. From energy management and savings to trust and data security, from healthcare and wellness to smart consumer devices, in the home, car and office, at work and at play, ST is found everywhere microelectronics make a positive and innovative contribution to people's life. By getting more from technology to get more from life, ST stands for life.augmented.
In 2012, the Company's net revenues were $8.49 billion. Further information on ST can be found at www.st.com.
Comcast RDK on ST STB Chiips:
For Press Information Contact:
Michael Markowitz
Director Technical Media Relations
+1 781 591 0354
[email protected]
SYS-CON Events announced today that robomq.io will exhibit at SYS-CON's @ThingsExpo, which will take place on June 9-11, 2015, at the Javits Center in New York City, NY. robomq.io is an interoperable and composable platform that connects any device to any application. It helps systems integrators and the solution providers build new and innovative products and service for industries requiring monitoring or intelligence from devices and sensors.
Mar. 30, 2015 06:00 PM EDT Reads: 1,539
Wearable technology was dominant at this year's International Consumer Electronics Show (CES) , and MWC was no exception to this trend. New versions of favorites, such as the Samsung Gear (three new products were released: the Gear 2, the Gear 2 Neo and the Gear Fit), shared the limelight with new wearables like Pebble Time Steel (the new premium version of the company's previously released smartwatch) and the LG Watch Urbane. The most dramatic difference at MWC was an emphasis on presenting wearables as fashion accessories and moving away from the original clunky technology associated with t...
Mar. 30, 2015 05:00 PM EDT Reads: 1,485
The list of 'new paradigm' technologies that now surrounds us appears to be at an all time high. From cloud computing and Big Data analytics to Bring Your Own Device (BYOD) and the Internet of Things (IoT), today we have to deal with what the industry likes to call 'paradigm shifts' at every level of IT. This is disruption; of course, we understand that – change is almost always disruptive.
Mar. 30, 2015 04:00 PM EDT Reads: 1,169
SYS-CON Events announced today that Solgenia will exhibit at SYS-CON's 16th International Cloud Expo®, which will take place on June 9-11, 2015, at the Javits Center in New York City, NY, and the 17th International Cloud Expo®, which will take place on November 3–5, 2015, at the Santa Clara Convention Center in Santa Clara, CA. Solgenia is the global market leader in Cloud Collaboration and Cloud Infrastructure software solutions. Designed to "Bridge the Gap" between Personal and Professional Social, Mobile and Cloud user experiences, our solutions help large and medium-sized organizations dr...
Mar. 30, 2015 03:00 PM EDT Reads: 2,931
The world's leading Cloud event, Cloud Expo has launched Microservices Journal on the SYS-CON.com portal, featuring over 19,000 original articles, news stories, features, and blog entries. DevOps Journal is focused on this critical enterprise IT topic in the world of cloud computing. Microservices Journal offers top articles, news stories, and blog posts from the world's well-known experts and guarantees better exposure for its authors than any other publication. Follow new article posts on Twitter at @MicroservicesE
Mar. 30, 2015 12:00 PM EDT Reads: 1,518
SYS-CON Events announced today the IoT Bootcamp – Jumpstart Your IoT Strategy, being held June 9–10, 2015, in conjunction with 16th Cloud Expo and Internet of @ThingsExpo at the Javits Center in New York City. This is your chance to jumpstart your IoT strategy. Combined with real-world scenarios and use cases, the IoT Bootcamp is not just based on presentations but includes hands-on demos and walkthroughs. We will introduce you to a variety of Do-It-Yourself IoT platforms including Arduino, Raspberry Pi, BeagleBone, Spark and Intel Edison. You will also get an overview of cloud technologies s...
Mar. 30, 2015 11:00 AM EDT Reads: 2,154
SYS-CON Events announced today that SafeLogic has been named "Bag Sponsor" of SYS-CON's 16th International Cloud Expo® New York, which will take place June 9-11, 2015, at the Javits Center in New York City, NY. SafeLogic provides security products for applications in mobile and server/appliance environments. SafeLogic's flagship product CryptoComply is a FIPS 140-2 validated cryptographic engine designed to secure data on servers, workstations, appliances, mobile devices, and in the Cloud.
Mar. 30, 2015 11:00 AM EDT Reads: 1,528
After making a doctor's appointment via your mobile device, you receive a calendar invite. The day of your appointment, you get a reminder with the doctor's location and contact information. As you enter the doctor's exam room, the medical team is equipped with the latest tablet containing your medical history – he or she makes real time updates to your medical file. At the end of your visit, you receive an electronic prescription to your preferred pharmacy and can schedule your next appointment.
Mar. 30, 2015 10:00 AM EDT Reads: 905
Containers and microservices have become topics of intense interest throughout the cloud developer and enterprise IT communities. Accordingly, attendees at the upcoming 16th Cloud Expo at the Javits Center in New York June 9-11 will find fresh new content in a new track called PaaS | Containers & Microservices Containers are not being considered for the first time by the cloud community, but a current era of re-consideration has pushed them to the top of the cloud agenda. With the launch of Docker's initial release in March of 2013, interest was revved up several notches. Then late last...
Mar. 30, 2015 09:15 AM EDT Reads: 2,262
The WebRTC Summit 2014 New York, to be held June 9-11, 2015, at the Javits Center in New York, NY, announces that its Call for Papers is open. Topics include all aspects of improving IT delivery by eliminating waste through automated business models leveraging cloud technologies. WebRTC Summit is co-located with 16th International Cloud Expo, @ThingsExpo, Big Data Expo, and DevOps Summit.
Mar. 30, 2015 09:00 AM EDT Reads: 1,649
SOA Software has changed its name to Akana. With roots in Web Services and SOA Governance, Akana has established itself as a leader in API Management and is expanding into cloud integration as an alternative to the traditional heavyweight enterprise service bus (ESB). The company recently announced that it achieved more than 90% year-over-year growth. As Akana, the company now addresses the evolution and diversification of SOA, unifying security, management, and DevOps across SOA, APIs, microservices, and more.
Mar. 30, 2015 08:30 AM EDT Reads: 2,084
GENBAND has announced that SageNet is leveraging the Nuvia platform to deliver Unified Communications as a Service (UCaaS) to its large base of retail and enterprise customers. Nuvia's cloud-based solution provides SageNet's customers with a full suite of business communications and collaboration tools. Two large national SageNet retail customers have recently signed up to deploy the Nuvia platform and the company will continue to sell the service to new and existing customers. Nuvia's capabilities include HD voice, video, multimedia messaging, mobility, conferencing, Web collaboration, deskt...
Mar. 30, 2015 01:00 AM EDT Reads: 1,506
SYS-CON Media announced today that @WebRTCSummit Blog, the largest WebRTC resource in the world, has been launched. @WebRTCSummit Blog offers top articles, news stories, and blog posts from the world's well-known experts and guarantees better exposure for its authors than any other publication. @WebRTCSummit Blog can be bookmarked ▸ Here @WebRTCSummit conference site can be bookmarked ▸ Here
Mar. 29, 2015 10:00 PM EDT Reads: 1,849
SYS-CON Events announced today that Cisco, the worldwide leader in IT that transforms how people connect, communicate and collaborate, has been named "Gold Sponsor" of SYS-CON's 16th International Cloud Expo®, which will take place on June 9-11, 2015, at the Javits Center in New York City, NY. Cisco makes amazing things happen by connecting the unconnected. Cisco has shaped the future of the Internet by becoming the worldwide leader in transforming how people connect, communicate and collaborate. Cisco and our partners are building the platform for the Internet of Everything by connecting the...
Mar. 29, 2015 07:00 PM EDT Reads: 5,277
Temasys has announced senior management additions to its team. Joining are David Holloway as Vice President of Commercial and Nadine Yap as Vice President of Product. Over the past 12 months Temasys has doubled in size as it adds new customers and expands the development of its Skylink platform. Skylink leads the charge to move WebRTC, traditionally seen as a desktop, browser based technology, to become a ubiquitous web communications technology on web and mobile, as well as Internet of Things compatible devices.
Mar. 29, 2015 06:00 PM EDT Reads: 1,880
Docker is an excellent platform for organizations interested in running microservices. It offers portability and consistency between development and production environments, quick provisioning times, and a simple way to isolate services. In his session at DevOps Summit at 16th Cloud Expo, Shannon Williams, co-founder of Rancher Labs, will walk through these and other benefits of using Docker to run microservices, and provide an overview of RancherOS, a minimalist distribution of Linux designed expressly to run Docker. He will also discuss Rancher, an orchestration and service discovery platf...
Mar. 29, 2015 04:15 PM EDT Reads: 2,459
SYS-CON Events announced today that Vitria Technology, Inc. will exhibit at SYS-CON's @ThingsExpo, which will take place on June 9-11, 2015, at the Javits Center in New York City, NY. Vitria will showcase the company's new IoT Analytics Platform through live demonstrations at booth #330. Vitria's IoT Analytics Platform, fully integrated and powered by an operational intelligence engine, enables customers to rapidly build and operationalize advanced analytics to deliver timely business outcomes for use cases across the industrial, enterprise, and consumer segments.
Mar. 29, 2015 03:30 PM EDT Reads: 2,206
SYS-CON Events announced today that Liaison Technologies, a leading provider of data management and integration cloud services and solutions, has been named "Silver Sponsor" of SYS-CON's 16th International Cloud Expo®, which will take place on June 9-11, 2015, at the Javits Center in New York, NY. Liaison Technologies is a recognized market leader in providing cloud-enabled data integration and data management solutions to break down complex information barriers, enabling enterprises to make smarter decisions, faster.
Mar. 29, 2015 03:00 PM EDT Reads: 3,504
@ThingsExpo has been named the Top 5 Most Influential M2M Brand by Onalytica in the 'Machine to Machine: Top 100 Influencers and Brands.' Onalytica analyzed the online debate on M2M by looking at over 85,000 tweets to provide the most influential individuals and brands that drive the discussion. According to Onalytica the "analysis showed a very engaged community with a lot of interactive tweets. The M2M discussion seems to be more fragmented and driven by some of the major brands present in the M2M space. This really allows some room for influential individuals to create more high value inter...
Mar. 29, 2015 01:45 PM EDT Reads: 4,699
SYS-CON Events announced today that Akana, formerly SOA Software, has been named "Bronze Sponsor" of SYS-CON's 16th International Cloud Expo® New York, which will take place June 9-11, 2015, at the Javits Center in New York City, NY. Akana's comprehensive suite of API Management, API Security, Integrated SOA Governance, and Cloud Integration solutions helps businesses accelerate digital transformation by securely extending their reach across multiple channels – mobile, cloud and Internet of Things. Akana enables enterprises to share data as APIs, connect and integrate applications, drive part...
Mar. 28, 2015 04:15 PM EDT Reads: 1,580


text:
Squashing ProSal myths
One of the most common questions I'm asked is how to compensate associate veterinarians properly. Some time ago, I developed a method called ProSal, which combines a guaranteed salary base with a percentage of an associate's production. It's now one of the most common forms of compensation used in veterinary practices, but it's often misunderstood or inappropriately applied. Practice owners say, "We pay our associates based on the ProSal method," but when I dig a little more, it turns out to be some mutant system and not ProSal at all. Let's see if we can clarify how ProSal is supposed to work and squash some of the common myths.
First, some definitions. Production is defined as "the fees generated and collected for services or products a doctor is directly involved in delivering." Here's the important distinction: The doctor must be involved in delivering a service or product in order to receive credit for it.Here's how it works: Let's assume Dr. Smith earns 21 percent of her production with a guaranteed base salary of $70,000. She'll receive production pay for any services she's directly involved in. So, for example, if she's in the exam room and conducts a comprehensive physical exam, administers vaccinations, performs fecal and heartworm tests, and sells preventive medicines, she'll receive 21 percent of the total revenue from those services and products, because she was directly involved in delivering them.
However, when the client returns a month later for a refill and doesn't see Dr. Smith during the visit, Dr. Smith won't get a percentage of that sale because she wasn't directly involved in the transaction. To clarify this further, I've developed a worksheet that lists the most common sources of production income and states whether credit goes to the doctor or the hospital. Download the "Crediting doctor production" PDF by clicking here. To keep production straight, create two provider codes for each doctor in your computer system—for example, "Dr. Smith" and "Dr. Smith: Rx." Use the latter code for refills the doctor doesn't get credit for. This code helps the receptionist and bookkeeper keep accurate production records but still ensures that the doctor's name is on the prescription label.
The going rate for production percentages is anywhere from 18 percent to 25 percent. In general, the greater the number of benefits you offer your associates, the less their production percentage should be; the fewer the benefits, the greater their percentage. No matter what production rate you pay, a doctor's total compensation—including health insurance, dues, licensing fees, continuing education, FICA matching, and other costs of employment—should not exceed 25 percent of his or her production.
Your first step is to figure out your associate's current total compensation—in other words, your total cost to employ him or her. To do this, use a total compensation statement. (Click here for an Excel spreadsheet to get you started.) This form lists possible costs associated with employing an associate doctor. Total these costs, then add the associate's current production compensation (W-2 income), and divide by the associate's total production. The resulting number is the associate's total compensation rate, which shouldn't exceed 25 percent. If it does, you're paying the associate out of your pocket and reducing your return on investment.
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You might be surprised by what your clients are researching. Plus, get an educational client handout.

subset: commoncrawl


text:
(Updated, 5:30 p.m.) Gov. Gina M. Raimondo will propose three programs designed to make college more affordable and easier to access in Rhode Island, and to attract and retain recent graduates in high-wage science, technology and design fields. more
By Mary MacDonald
Two Rhode Island-based companies, Alex and Ani and First Point Power, made the top 100 in Inc. Magazine's annual ranking of the 5,000 fastest-growing private companies in the country, released Wednesday. more
By Kaylen Auer
Nabsys Inc. has named Tony Shuber vice president and chief scientific officer in its latest move toward bringing its genome-mapping products to market. more
By Gabrielle Porter
Leaders of small businesses eager to win Small Business Innovation Research grants asked a federal administrator at a roundtable Thursday to take steps to help them navigate the complex process. more
By Patricia Daddona
After startups from France's Vente-Privee.com SA to the U.K.'s Hailo Network Ltd. retreated from the United States last year, European entrepreneurs are learning just how hard crossing the Atlantic can be. more
By Amy Thomson and Marie Mawad
Two Rhode Islanders will be honored among more than 50 Global Enterprising Educators and Global Young Entrepreneurs receiving awards at the 2014 Network for Teaching Entrepreneurship Gala. more
By PBN Staff
The Newport County Mentor/Co-op Group has asked the R.I. Department of Education to consider supporting an advanced manufacturing academy, a charter school, based in Newport County. more
By Patricia Daddona
Jewelry marketer and distributor Richline Brands, a subsidiary of Berkshire Hathaway Inc., has announced strategic partnerships with two companies as part of an effort to offer "smart" fine jewelry to retailers. more
By PBN Staff
Wouldn't we all like to find ourselves at the top of a list that signifies rapid growth? Now in its third year, the Fastest Growing & Innovative Companies program presents the opportunity to do just that. more
By Mark S. Murphy
Gannon & Scott Inc.'s business strategy can be summed up in two words: green growth. more
By Sarah Parsons
Contributing Writer | 4/28/14


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- Resources
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- Earth Surface & Interior
I will determine interseismic strain accumulation in space and time across metropolitan Los Angeles, comprehensively analyzing the 250 permanent GPS sites in the Southern California Integrated GPS Network and all available geodetic data, including trilateration, campaign GPS, and other PBO data. As of 2007 I have, on the basis of at least five years data, estimated the velocities of 240 permanent GPS sites, many more than the 42 in Argus et al. [2005] and the 36 in Southern California Earthquake Center Crustal Motion Map version 3 based on this much data. This is resulting in significant science advance. I will: (1) Determine the distribution of reverse slip between the Puente Hills, Sierra Madre, and other metropolitan Los Angeles thrust faults, (2) Use finite element (GeoFEST, PyLITH) and analytic (EDGRN/EDCMP) models of elastic strain accumulation to evaluate the effect of the Los Angeles sedimentary basin on estimates of slip rates and locking depths, (3) Estimate the slip rate and locking depth of the Mojave segment of the San Andreas fault because four published estimates all differ significantly, (4) Roughly correct site velocities for water and oil management and natural water phenomena, and (5) Determine, and compare with prior models, a model of southern California specifying the angular velocities of about 25 elastic blocks and the slip rates and locking depths of the faults between the blocks. This research fulfills NASA's goals of better forecasting the likelihood and location of earthquakes, understanding the dynamics driving deformation, and determining Earth's response to tectonics, climate, and man.
Project PI: Donald Argus/Jet Propulsion Laboratory
Jet Propulsion Laboratory, 4800 Oak Grove Dr. Pasadena, CA 91109 United States
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Fifty Shades of Grey: An International Appeal
The runaway success of E.L. James' Fifty Shades of Grey has exposed some of America's other sexual impulses. The trilogy has sold tens of millions of copies by appealing to readers of so-called "mommy porn".
Last month, the books made an astounding debut in France… we caught up with Jason Boog, editor of the publishing website Galley Cat and our publishing industry mole for more on sales.
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RUMOUR: Has Remedy's Xbox One exclusive been delayed to next tear?... Continue Reading
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Why Going Free-To-Play Is The Best Thing For Fable Legends
Fable Legends will be free-to-play and that's great news for all... Continue Reading
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RARE Has "Multiple Projects In Development," Reveals Microsoft
What will RARE have to show off at E3 2015?... Continue Reading
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Some games might need to be delayed to 2016 to help alleviate the overcrowding problem... Continue Reading
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Forza Motorsport to launch in 2015 ... Continue Reading
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Reports are surfacing today that the release of Xbox One exclusive Phantom Dust is in jeopardy following the closure of developer Darkside Game Studios... Continue Reading
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Recent answers to Emailed Videos won't play, but will on Internet Explorerhttps://support.mozilla.org/en-US/questions/9471622013-01-15T15:36:28-08:00Is the video inside your email or does it link you out to another place? Are your plugins up to dat2013-01-15T15:36:28-08:00feer56https://support.mozilla.org/en-US/questions/947162#answer-398168
Is the video inside your email or does it link you out to another place? Are your plugins up to date?

Please check if all your plugins are up-to-date. To do this, go to the Mozilla Plugin Check site.

Once you're there, the site will check if all your plugins have the latest versions. If you see plugins in the list that have a yellow Update button or a red Update now button, please update these immediately.

To do so, please click each red or yellow button. Then you should see a site that allows you to download the latest version. Double-click the downloaded file to start the installation and follow the steps mentioned in the installation procedure.


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We found 4 sites within 32 miles of Pewsey with 0 bookable
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Special Offer:
Buy any three DVD's and receive a free Milan San Remo DVD featuring Mark Cavendish winning the Italian classic
DVDs now only £14.99
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Indoor cycling training workout DVDs & video downloads featuring pro riders Mark Cavendish & Pete Kennaugh. Suitable for turbo trainers, exercise bikes, spin bikes & bike rollers. The 3LC DVD collection of cycling workout and training sessions have been designed to appeal to cyclists of all ages and abilities. These cycling training dvds will help to improve endurance, cycling techniques, overall strength & weight loss.


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Google Panda, the Samsung smart knife, and more: Because even corporate America likes to pull one over on us.
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Page 1
Denitrifying Bacterial Community Composition Changes
Associated with Stages of Denitrification in Oxygen
Minimum Zones
A. Jayakumar & G. D. O'Mullan & S. W. A. Naqvi &
B. B. Ward
Received: 4 August 2008 /Accepted: 12 January 2009 /Published online: 24 February 2009
# Springer Science + Business Media, LLC 2009
Abstract Denitrification in the ocean is a major sink for
fixed nitrogen in the global N budget, but the process is
geographically restricted to a few oceanic regions, includ-
ing three oceanic oxygen minimum zones (OMZ) and
hemipelagic sediments worldwide. Here, we describe the
diversity and community composition of microbes respon-
sible for denitrification in the OMZ using polymerase chain
reaction, sequence and fragment analysis of clone libraries
of the signature genes (nirK and nirS) that encode the
enzyme nitrite reductase, responsible for key denitrification
transformation steps. We show that denitrifying assemb-
lages vary in space and time and exhibit striking changes in
diversity associated with the progression of denitrification
from initial anoxia through nitrate depletion. The initial
denitrifying assemblage is highly diverse, but succession on
the scale of 3–12 days leads to a much less diverse
assemblage and dominance by one or a few phylotypes.
This progression occurs in the natural environment as well
as in enclosed incubations. The emergence of dominants
from a vast reservoir of rare types has implications for the
maintenance of diversity of the microbial population and
suggests that a small number of microbial dominants may
be responsible for the greatest rates of transformations
involving nitrous oxide and global fixed nitrogen loss.
Denitrifying blooms, driven by a few types responding to
episodic environmental changes and distributed unevenly in
time and space, are consistent with the sampling effect
model of diversity–function relationships. Canonical deni-
trification thus appears to have important parallels with
both primary production and nitrogen fixation, which are
typically dominated by regionally and temporally restricted
blooms that account for a disproportionate share of these
processes worldwide.
Diverse assemblages of microbes perform important bio-
geochemical transformations in the ocean such as the
removal of fixed N by denitrification. The ability to
denitrify occurs widely in many different taxonomic
groups, and molecular surveys show that natural denitrify-
ing assemblages usually contain many different phylotypes
[4, 21, 39]. It is often a challenge to identify the microbes
involved in these transformations and to understand the
significance of microbial diversity in contributing to the
rate and distribution of biogeochemical transformations
[19]. Denitrification refers to the process of removal of
fixed nitrogen through canonical denitrification and or
anammox. The term denitrifying bacteria refers to cells
that perform heterotrophic denitrification. We use the term
canonical denitrification to refer to the sequential reduction
of nitrate to nitrite, then nitric and nitrous oxides, and then
Microb Ecol (2009) 58:350–362
DOI 10.1007/s00248-009-9487-y
A. Jayakumar:B. B. Ward (*)
Department of Geosciences, Guyot Hall, Princeton University,
Princeton, NJ 08544, USA
e-mail: email@example.com
A. Jayakumar
e-mail: firstname.lastname@example.com
G. D. O'Mullan
School of Earth and Environmental Sciences, Queens College,
City University of New York,
Flushing, NY 11367, USA
e-mail: firstname.lastname@example.com
S. W. A. Naqvi
National Institute of Oceanography,
Dona Paula, Goa 403004, India
e-mail: email@example.com
Page 2
to dinitrogen gas, an anaerobic respiratory process carried
out by heterotrophic microbes.
Denitrification occurs in hemipelagic sediments and in
low oxygen regions of the water column. The three major
oceanic oxygen minimum zones (OMZs) located in the
Arabian Sea, the eastern tropical North Pacific (ETNP) and
the eastern tropical South Pacific (ETSP) contain only 0.1–
0.2% of the total volume of the ocean, but they are important
sources of nitrous oxide (N2O), a potent greenhouse gas to
the atmosphere, and account for about 30% of the oceanic
fixed nitrogen loss as N2[8]. Canonical denitrification has
long been considered to be the principal pathway by which
fixed nitrogen is removed in these regions. However, recent
discoveries suggest that anaerobic ammonia oxidation
(anammox) is also an important, even dominant, pathway
of N2production [24, 46].
The Arabian Sea covers only 2% of the surface area of
the oceans, but its OMZ, the thickest found anywhere in the
world, accounts for 40% of the global pelagic N2
production, thereby making a disproportionate contribution
to the marine nitrogen budget [3]. The widespread open-
ocean oxygen deficiency in this region results from a
combination of a high oxygen demand, arising from high
biological productivity in the surface waters, and the
limited supply of oxygen to intermediate waters. In addition
to the perennial open-ocean OMZ, oxygen deficient
conditions also develop seasonally over the continental
shelf of India. Between May and November, upwelling
brings low-oxygen water over this shelf, and the respiration
of locally produced organic matter in conjunction with
strong stratification leads to intense denitrification followed
by sulphate reduction at very shallow depths. An unusual
feature of the coastal OMZ is the accumulation of N2O in
very high concentrations, which drives the highest N2O
flux to the atmosphere reported from the world oceans [30].
Most of the N2O in the coastal system appears to be
produced through canonical denitrification.
Denitrification rates have rarely been measured directly
in the oceanic OMZs [12], but the denitrifying waters are
readily recognized by an accumulation of nitrite (secondary
nitrite maximum (SNM)) and a partial depletion of nitrate
(nitrate deficit). The intensity of these signals is assumed to
correlate with denitrification rates [15]. The objective of
this study was to relate the diversity of the denitrifying and
anammox assemblages to the intensity of denitrification as
indicated by the proxy signals of nitrite and nitrate deficit.
In the Arabian Sea, the SNM is located in the 150–400 m
depth range, where the Winkler oxygen concentration is
<0.1 ml L−1(the OMZ can span up to the depth interval
from ∼100 to 1,200 m). Although the SNM is assumed to
be the site of most intense denitrification and the OMZ
regions of the Arabian Sea have been well characterized
geochemically, very little is known about the microbes that
are responsible for the observed characteristic chemical
We hypothesized that variations in community compo-
sition of denitrifying phylotypes should be related to the
redox state of the water column, characterized in terms of
different stages of denitrification (Table 1). The community
composition and structure is hypothesized to change from a
high diversity assemblage present at the induction of
denitrification into a low diversity, high abundance assem-
blage as denitrification intensifies. Thus, low-diversity
assemblages should dominate in areas associated with high
nitrite concentrations, high nitrate deficits, and thus inferred
regions of high N2flux, while higher-diversity assemblages
are found in earlier stages of denitrification. We investigat-
ed the composition of denitrifier and anammox assemblages
in the OMZ by analyzing the marker genes nirS and nirK
involved in the denitrification process and the 16S rRNA
gene identified with anammox bacteria. Details of phylo-
genetic analysis of nirK, nirS, and anammox 16S rRNA are
presented elsewhere [21, 22]. On the basis of large-scale
patterns of diversity observed in the sequence and restric-
tion fragment data from individual stations, we now
document the predicted correlation of denitrifier assem-
blage diversity with the progression of denitrification at
both open-ocean and coastal stations in the Arabian Sea.
Materials and Methods
Study Area and Sample Collection
Three open-ocean stations (1, 2, 23) and two coastal stations
(K03, 17) were sampled on ORV Sagar Kanya cruises
SK208 and SK209 in the Arabian Sea between August and
October 2004. Coastal stations (G8 and V4) were sampled
during a cruise on the RV Sagar Sukti in October 2001.
Historical data on cell counts and nitrite concentrations are
included from an earlier cruise, ORV Sagar Sampada
cruise SS150 (November–December 1996). Station loca-
tions are shown in Fig. 1 and given in Table 2.
Table 1 Criteria for assignment of denitrification stage
Stage of
Nitrite concentration
% of NO3−reduced
100% (not SO4−reducing)
Denitrifying Bacterial Bloom Dynamics 351
Page 3
Water-column sampling and temperature/salinity profiling
were carried out using a Sea-Bird Electronics Conductivity–
Temperature–Depth rosette sampling system, Model SBE9,
fitted with Niskin/Go-Flo bottles. Previous work in this area
had identified strong correlations between nitrite, particle, and
oxygen concentrations [29, 33]), so we used nitrite concen-
tration as a proxy to define the depth extent of the OMZ.
Water samples from an initial cast were quickly analyzed for
nitrite content (manual spectrophotometry). Samples for
further analysis were then collected to bracket the core of
the OMZ. Nutrient analyses were carried out onboard ship
using a Skalar auto analyzer [16], and dissolved oxygen
(DO) concentrations were determined by the titrimetric
Winkler method [7] on discrete water samples from the
complete depth profile.
Bag Incubations
To monitor denitrifier community composition associated
with the progression of denitrification and the resulting
changes in concentration of dissolved inorganic nitrogen
(DIN) species, we carried out bag incubations during cruises
SK208 and SK209. Four samples from the core of the OMZ
at stations K03, 1, 2, and 17 were collected using aseptic,
trace metal clean techniques without atmospheric contami-
nation and incubated in trace metal clean airtight plastic
laminate bags at close to in situ temperatures (24°C—Station
K03 and 15°C—stations 1, 2, and 17) with no additions of
any substrates or other treatments. Small aliquots of water
samples were drawn from these bags with airtight syringes
once daily, and nitrate, nitrite, nitrous oxide, and cell
numbers were measured in the bag samples by the methods
used for whole water samples (above). Samples for DNA
were collected from the incubation bag at station K03 after
32and 60hofincubationand from bagsincubatedatstations
1, 2, and 17 after 208, 310, and 159 h, respectively.
Microbial Abundance
Samples from SS150, preserved in formalin (2% v/v final
concentration) were enumerated for microbial abundance
using 4′,6-diamidino-2-phenylindole staining and epifluor-
escence microscopy[37]. Samples collected on SK209 were
preserved in glutaraldehyde (2% v/v final concentration),
Table 2 Station locations and hydrographic and nutrient data for stations from which clone libraries were made
Sample Sample depth
Station depth
Lat °NLong
StageST (oC)[NO3−]
0 167
20 83
Stage stage of denitrification as defined in the text and in Table 2, DO dissolved oxygen concentration measured colorimetrically
Figure 1 Study region in the Arabian Sea. Station locations for
cruises SS150 in 1996; SK208 (closed circles station K03) and SK209
(closed circles stations 1, 2, 17, and 23) in September–October 2004,
and for Sagar Sutki October 2001 (closed diamonds stations G8 and
V4) are shown. Dotted line denotes the region where [NO2−] exceeds
0.5 μM in the oxygen minimum zone region. Stations 1 and 2 were
occupied on both SS150 and SK209
352A. Jayakumar et al.
Page 4
and cell density was estimated by flow cytometry using
Syto 13 dye (Invitrogen) and a Benton Dickinson FACSort
with a 488 nm laser.
Nucleic Acid Manipulations and Diversity Analysis
During cruises SK208 and SK209, particulate material from
5–10 L seawater was collected onto Sterivex capsules
(0.2 μm filter, Millipore, Inc., Bedford, MA, USA) with a
peristaltic pump. Particulate material from 4 L of seawater
from the bag incubations was collected by filtration onto
Sterivex capsule filters. Immediately after filtration, the
capsule filters were quick frozen in liquid nitrogen and
stored at −80°C until the DNA could be extracted.
DNA extraction techniques, polymerase chain reaction
(PCR) conditions for nirS and nirK, the construction and
analysis of clone libraries, and restriction fragment length
polymorphism (RFLP) methods have been described
previously [21, 38]. For this study, clone libraries were
constructed from five environmental samples and four
incubation samples (Table 3). Primers designed for the
major anammox groups (AMX 368F and AMX820R) [41]
were used to amplify anammox 16S rRNA genes. Clones
were randomly selected from the libraries and sequenced
using an ABI 310 Genetic Analyzer without additional
screening. All the clone libraries were constructed from
initial (natural) samples except for the latter two time points
from Station K03 and final time points from stations 1 and
17, which were constructed from samples taken from the
incubation bags at the times indicated (Table 3). Sequences
were edited and assembled using Sequencher 4.1 (Gene
Codes Corporation, Ann Arbor, MI, USA). Phylogenetic
analysis was performed using DNA alignments for the 16S
rRNA anammox sequences and for nirS and nirK sequen-
ces for diversity and operational taxonomical unit (OTU)
analysis. DNA sequences were translated into amino acid
sequences and used for phylogenetic analysis of nirS and
nirK genes. Multiple alignments were created in Clustal X
[47], and neighbor-joining trees were produced using
distance matrix methods (PAUP 4.0, Sinauer Associates).
Bootstrap analysis was used to estimate the reliability of
phylogenetic reconstruction (1,000 replicates). Twenty-one
of the 307 nirS nucleotide sequences were aligned separately
because of greater divergence, but these sequences were
confirmed to be nirS based upon translated amino acid
sequences and were included in further analyses. nirS
sequences from the coastal Arabian Sea [21] are also
included in the diversity analysis. To estimate the level of
identity with the published sequences, all sequences gener-
ated in this study were compared to the National Center for
Biotechnology Information (http://www.ncbi.nlm.nih.gov/)
database sequences using BLAST search.
Table 3 Details of nirS, nirK, and anammox clone sequence data and diversity indices from the OMZ of the Arabian Sea
StagenirSnirKAnammox 16S rRNA
Station# of
# of
# of
# of
# of
# of
V4 – 0a
6 0.97
9 0.571.25
43 25
ND PCR amplification attempted, but no product was detected; NA PCR amplification was not attempted on these samples; + PCR amplification
was successful, but clone libraries were not constructed; J Pielou's J index of dominance; H′ Shannon–Wiener index of diversity; V4 station 4 off
Vengurla, India; G8 station G8 off Goa, India
aNumbers that follow the Station Number indicates the sample depth
Denitrifying Bacterial Bloom Dynamics 353
Page 5
The nirS and nirK OTUs were calculated from the
combined station database using the furthest neighbor
algorithm in the DOTUR software package [40]. Unique
OTUs were defined to include DNA sequences with >90%
identity to each other for nirS and nirK. For anammox 16S
rRNA, the OTU definition was 99% identity. OTU
frequencies (Pi) were normalized to the number of clones
from the sample that were sequenced from the library, such
that Pi = number of sequences from a library belonging to
OTUi divided by the total number of clones sequenced
from the library. Shannon–Wiener (H′) and Pielou's J (J)
indices were calculated in Excel for each gene at each site
using the equations H′ = −∑ Pi (log Pi) and J = H′/(log
average OTU richness), respectively [27]. Dominance is
quantified as 1−Pielou's J. Beta diversity is reported as the
total combined richness for the group of sites divided by the
average richness for the sites.
Restriction fragment length polymorphism analysis was
used to supplement clone library sequence data for
characterizing the changes in diversity during bag incuba-
tions initiated with samples from stations 1, 2, and 17.
Representatives of each RFLP pattern generated from the
clone libraries were partially sequenced to confirm that the
fragments did indeed represent nirK or nirS sequences, but
not all clones corresponding to each of these RFLP patterns
were sequenced from both ends. Rarefaction statistics [17]
were computed using the software Analytic Rarefaction
1.3TM [18] and OTUs were defined on the basis of distinct
RFLP patterns.
Accession numbers are reported here for the nirK
(EU069625–EU069754) and the anammox 16S rRNA
(EU069755–EU069813) sequences. Detailed phylogenetic
analysis and accession numbers for the members of the
clusters of nirS and nirK amino acid sequences will be
presented elsewhere [22].
Stages of Denitrification
Using nutrient and hydrographic criteria, we have assigned
discrete stages of denitrification to water column conditions
representing the progressive development of denitrification
(Table 1, Fig. 2a). Based on the chemical features that
characteristically develop during the mineralization of
organic matter, a numerical index was assigned to denote
the stages in the progression of oxidized N species
associated with denitrification using nitrite concentration
and nitrate removed (calculated according to [8]). In an oxic
environment, nitrate coexists with dissolved oxygen (stage 0).
When DO is depleted (<5 μM) and suboxia develops
(stage 1), denitrifiers take over the remineralization
process, reducing nitrate and thereby producing traces of
nitrite, nitrous oxide, and molecular nitrogen as interme-
diate and terminal products. As low oxygen conditions
persist over time, nitrite initially accumulates, sometimes
with a transient accumulation of nitrous oxide (stage 2),
but nitrite is subsequently reduced (stage 3), and eventu-
ally most of the nitrate is converted to nitrite and further to
Figure 2 The stages of denitrification. a Cartoon representing relative
concentrations of nitrate, nitrite, and molecular nitrogen as a function
of stage of denitrification. b Variation in H′ with stage of
denitrification. Data include nirK (open triangles) and nirS (open
diamonds), coastal [21] and open ocean (SK209), and samples from
both bag incubations and in situ conditions. c Dominance index for all
samples in b
354A. Jayakumar et al.
Page 6
N2O or N2 (stage 4). As complete anoxia occurs, all
oxidized forms of nitrogen are reduced to N2(stage 5).
Stage 6 signifies the occurrence of sulfate reduction and is
common in marine sediments but is rarely reached in
water column environments. Hydrographic data for the
stations under investigation are presented in Table 2, along
with their assignment to a stage of denitrification.
Bacterial Abundance and Stage of Denitrification
Microbial cell abundance maxima typically occurred within
the SNM (Fig. 3). Cell abundance is also related to
denitrification stage (Fig. 4a, b). Scatter in these data sets
is partly due to the unimodal distribution of nitrite
concentration over the progression of denitrification, i.e.,
nitrite disappears again at the very late stages of denitrifi-
cation and also due to intrusion of Persian Gulf water into
the OMZ water of the Arabian Sea, thus mixing two water
masses with different cell number–nitrite relationships. In
addition, the assignment of stages is somewhat complicated
because it combines the net result of the history of the water
and in situ microbial activity.
Diversity of Denitrifying Bacteria in the OMZ Based
on Key Denitrification Genes, nirK and nirS
All samples were successfully amplified with primers
designed for the gene encoding bacterial 16S rRNA,
verifying that amplifiable DNA was obtained from all
samples. nirK could be amplified from all seven samples
from which amplification was attempted, including all the
incubated samples, while nirS could be amplified only from
the three open-ocean samples and six of the eight coastal
samples (samples representing the later stages of denitrifi-
cation; Table 3). nirK analysis was not attempted for the
stations reported by Jayakumar et al. [21].
Phylogenetic trees were constructed from nirK (seven
samples from both coastal and open-ocean stations; 278
sequences) and nirS (three open-ocean samples, stations 1, 2,
and 23; 175 sequences) gene fragments from the clone
libraries made from SK208 and SK209 samples collected in
Jayakumar et al. 2004 [22]. The present analysis relies on
OTUs defined from this collection of sequences plus those
obtained from the coastal stations previously from samples
V4-0, V4-83, G8-40, and G8-57 in October 2001 [21]
(Table 3). The patterns are further supported by nirS and
nirK RFLP data collected from bag incubations (stations 1
and 17) and by the sequence analysis from the bag
incubations at station K03.
Figure 3 Depth distribution of water column chemistry associated with
OMZ/denitrification and cell abundances at station 1 (17° N, 68° E) in
1996 (SS150). Plus signs nitrate, open triangles nitrite, closed circles
microbial abundance, open diamonds dissolved oxygen
Figure 4 a Microbial abundance (in situ samples) from cruise SS150
(November 1996, Arabian Sea) plotted as a function of stage of
denitrification. b Microbial abundance from cruise SK209 (October
2004, Arabian Sea) plotted as a function of stage of denitrification.
Data are from both in situ samples and bag incubations
Denitrifying Bacterial Bloom Dynamics355
Page 7
The open-ocean environment harbored less nirS diversi-
ty (13 OTUS total, 11 OTUs specific to oceanic libraries;
beta diversity=1.5) than the coastal environment (32 OTUs
total, 30 OTUs specific to coastal libraries; beta diversity=
2.8) despite a slightly larger sequencing effort in the open-
ocean samples (Table 3). Only two OTUs representing 10%
of the total nirS sequences collected were detected in both
environments. The distribution of OTUs was more uniform
for nirK (open ocean=15 OTUs total, nine OTUs specific
to open-ocean libraries, beta diversity=1.7; coastal=16
OTUs total, ten OTUs specific to coastal libraries, beta
diversity=1.7). Only six OTUs representing 45% of the
total nirK sequences were detected in both coastal and
open-ocean samples, indicating that the two environments
harbor substantially different communities for both nirS and
nirK. The details of the phylogenetic diversity are presented
elsewhere [22].
The overall estimates of diversity presented here
(Table 3) are probably underestimates because no PCR
primers can be relied upon to detect or amplify all possible
related genes. The patterns we observed are therefore
considered within the constraints of the clone libraries and
may apply with variable accuracy to the natural assem-
blage. Nonetheless, consistent methodology has been
applied throughout allowing a robust relative comparison
of samples within the constraints of the primer sets and
with the caveat that not all primers amplify with same
efficiency and the sample matrix can inhibit PCR with
some primers and not others.
Progression of Denitrification
A wide range of environmental conditions, representing
different stages of denitrification, was encountered in the
open-ocean and coastal Arabian Sea stations (Table 2). The
open-ocean stations generally represented the earlier stages,
while later stages were found at the coastal stations. Station
1 represented the latest stage (stage 3) found among the
open-ocean stations, and it had intermediate levels of
dominance in both nirK and nirS in the ambient sample
(Table 3). Coastal station V4 had progressed through
complete nitrite + nitrate removal (stage 5, Table 2)
and exhibited strong dominance among nirS phylotypes
(Table 3). It represents a very late stage in denitrification,
perhaps even "post denitrification," despite the presence of
oxygen. The total absence of nitrate and nitrite reflects the
history of this water as recently upwelled to the surface
(thus replenishing its DO concentration), having recently
undergone denitrification in contact with shelf sediments,
and any residual nitrate having been consumed by
phytoplankton at the surface. The seasonal development
of denitrification in these shelf waters, accompanied by
very high nitrous oxide fluxes, has been documented [30].
In addition to sampling an environmental gradient that
represents the progression of denitrification, we also
explicitly followed the progressive development of denitri-
fication in incubations of natural samples in airtight bags
from stations K03, 1, and 17. No substrate additions were
made to these bags, so the developments depended entirely
upon the initial conditions. In both the Eastern Tropical
North Pacific and the Eastern Tropical South Pacific OMZ
waters, no changes in dissolved inorganic nitrogen concen-
trations or cell number occurred over >8 days in control
bags with no additions of any substrates [50]. In the
Arabian Sea, however, denitrification occurred in the bags
soon after incubations were initiated, even when no carbon
was added. These results show that there was sufficient
organic carbon available in the Arabian Sea during the
sampling period to fuel denitrification, while both the
ETNP and ETSP were apparently carbon limited at the time
of the experiments [50].
The initial samplefromstation 17had the characteristics of
stage 0 (Table 2) but underwent complete denitrification
during the incubation, based on the near total consumption of
NO3−within 6 days. Over this period, the RFLP diversity of
nirK genes in the incubation decreased dramatically (Fig. 5).
Similar decrease in diversity of nirK genes was observed in
the incubated samples from station 1, as seen in the
rarefaction curves in Fig. 5. In both incubations, the initial
sample had 12 OTUs, and that number decreased to about
five OTUs in the later stages of denitrification.
Stage 0 was also represented by station K03 (shelf
region off Karwar; Table 2). Transformations occurred
rapidly in this incubation, probably due to the high in situ
organic matter content of waters in this region because of
Figure 5 Rarefaction curves of RFLP-defined OTUs for nirK clone
libraries from station 1 (closed circles, open circles) and 17 (closed
diamonds, open diamonds) before (initial water sample; closed
symbols) and at the end (open symbols) of the incubation (208 h for
station 1; 159 h for station 17)
356A. Jayakumar et al.
Page 8
Figure 6 Phylogenetic tree for nirK sequences obtained from a bag
incubation experiment at station K03 (cruise SK208, October 2004)
with sequences from all three time points (T0 no stars; T1=32 h,
single asterisks; T2=60 h, double asterisks). The nirK tree was based
on DNA sequences of approximately 470 bp. Bootstrap values
determined from 1,000 iterations are shown for nodes with >50%
support. Sequences from cultivated strains are shown in italics and a
few closely related database sequences are also included for reference.
The pie charts represent the distribution of OTUs (fraction of the
clone library) at each time point
Denitrifying Bacterial Bloom Dynamics 357
Page 9
the high primary productivity during this season [30]. The
phylogenetic distribution of nirK genes shows that the
diversity present in the initial time point decreased
dramatically as denitrification progressed in the bag
(Fig. 6). After 2.5 days, 40 out of 43 clones (93%) were
identical at the amino acid level. The diverse nirK
community present initially (H′=1.94) underwent succes-
sion as denitrification intensified in the incubation, leading
to a community dominated by one OTU (H′=0.29). The
nirS community responded similarly in the incubation: nirS
could not be amplified from the initial sample, so nirS data
from this experiment were not included in the diversity
analysis. nirS was, however, detected in the later timepoints
from the incubation; the nirS clone library generated from
the end point of this same incubation was dominated (67%
of total) by one nirS clone.
Community succession also occurred in incubations of
open-ocean water. Water incubated from station 1,
initially stage 3, underwent nearly complete denitrifica-
tion within 8 days (Fig. 7), and cell number increased to a
maximum coinciding with the reduction of nitrate and the
transient appearance of nitrous oxide. Initial nitrite in the
bags was slightly different from the ambient water column
concentration (Table 2) because the bags were filled from
a subsequent cast. By the end of the bag incubation at
station 1, the shape of the nirK rarefaction curve had
changed in a manner very similar to the change observed
at station 17 (Fig. 5), indicating a large reduction in
diversity. In the bag, succession led to the establishment of
strong dominance in which one phylotype (99% identical
at the amino acid level) comprised 52% of the final clone
Many of the nirS OTUs (128 of 175 sequences) occurred
at all three OMZ stations, but the dominant OTUs varied
geographically. Thus, different stages of denitrification
appear to be accompanied by different community compo-
sitions in the open-ocean OMZ. Similarly, even though
some of the same phylotypes were present in both the open-
ocean and coastal OMZ, the dominant OTUs differed. At
the DNA level, the dominant nirK OTU from the coastal
zone (from incubation experiments) had only 71% identity
to the dominant OTU from station 1, where the closest
match to cultured strains were Roseovarius sp. 217 (75%
identity) and Rhodobacterales bacterium HTCC2654 (80%
identity), respectively. Similarly for nirS, the dominant
OTU in the open ocean had only 76% identity to the
dominant sequence from the coastal zone, where the closest
match was to a cultivated strain, the anammox bacterium
Kuenenia stuttgartiensis (45% identity), for the open ocean
and Magnetospirillum magneticum AMB-1 (72% identity)
for the coastal zone.
Anammox Diversity
Very little variation in community composition and diver-
sity was detected in the anammox assemblage on the basis
of 16S rRNA analysis (Table 3). All 58 Arabian Sea
anammox sequences, from three clone libraries (stations 1,
2, and 23), were >98% identical, i.e., only one OTU was
detected with an identity cutoff of 98%. With an OTU
definition of 99% identity, a total of seven OTUs could be
distinguished, but the two most abundant OTUs in the
clone library contained 42 of the clones. Three of the OTUs
were present at all three open-ocean stations. Although
there is variation among groups, the conventional identity
for a species definition is 97% identify in 16S rRNA
sequence, so the anammox sequences here define a very
homogenous group.
The primers employed here were designed to detect the
main wastewater anammox genera, Brocadia anammoxidans
and K. stuttgartiensis, but only Scalindua was detected, and
only one phylotype of Scalindua could be distinguished. The
small sequence difference between these primers and those
"specific" for Scalindua was apparently not sufficient to
distinguish them or to discriminate against an abundant
phylotype. It is also possible, however, that not enough is
known about the extent of anammox bacterial diversity to
make truly universal primers, leading to an underestimation
of the anammox bacterial diversity.
We hypothesized the following scenario of changes in the
heterotrophic microbial community structure associated
Figure 7 DIN concentrations and cell numbers in 10-L bag
incubation experiment from Arabian Sea station 1 (2004). Data are
averages of three replicate incubations with no carbon additions.
Nitrate (closed diamonds), nitrite (open diamonds), nitrous oxide
(open circles), cell number (plus signs)
358A. Jayakumar et al.
Page 10
with stages in the induction and intensification of denitri-
fication following the transition from oxic to anoxic
conditions (Table 1). At stage 0, several different species
of denitrifiers are present, albeit in low numbers, and the
population is dominated by organisms that do not possess
nirK or nirS genes. The overall diversity is high, but
denitrifiers comprise a small part of the community. As the
oxygen concentration falls below the threshold for the onset
of denitrification (1–4 μM; [9, 11], conditions become
more favorable for denitrifiers and less favorable for
obligate aerobes. Hence, both the absolute and relative
abundance of denitrifying cells increase. Competition for
carbon substrates, and perhaps NO3−, among denitrifiers
becomes important, and selection starts to play a role in
determining the growth success of any particular denitrify-
ing type. In the later stages of denitrification (>3) where
cell number is the highest, differential selection leads to a
decrease in OTU diversity and an increase in dominance of
one or a few types of denitrifying organisms.
The coincidence of a microbial cell number maximum
with the subsurface particle maximum, the SNM, and the
nitrate deficit is a common feature in all three major OMZ
regions of the world oceans [14, 32, 36, 43]. Based on
particle size distributions and microbial cell abundance,
Spinrad et al. [43] concluded that most of the small
particles causing the transmission minimum (beam attenu-
ation measured with a transmissometer) in the ETSP were
indeed bacterial cells. The subsurface particle maximum
also coincides with the maximum in the activity of the
respiratory electron transport system (and particulate pro-
tein [43]. These earlier data suggest a relationship between
cell numbers and denitrification activity as inferred from
nitrite concentration in the OMZ.
The oxygen-depleted environment of the OMZ is not
conducive for the growth of aerobic heterotrophs, e.g., the
SAR11 cluster which comprises up to 26% of the bacterial
assemblage of the open-ocean realm [28]. Denitrifying
bacteria, however, use canonical denitrification as a
respiratory process that couples electron transport to the
stepwise sequential reduction of nitrogen oxides during
heterotrophic growth on organic matter. Thus, due to its
redox state, the OMZ environment is selective for deni-
trifying bacteria, and we hypothesize that the cell number
maxima associated with the SNM in the OMZ are
composed disproportionately of denitrifying cells compared
to the assemblage in surface waters. Cell abundances in the
OMZ approach the levels usually found in surface waters,
up to 10-fold higher than is normal for equivalent depths in
non-OMZ regions (Figs. 3, 4) [43]. Since denitrifying
bacteria are expected to account for less than 10% of the
total cells in non-OMZ regions but probably constitute the
vast majority cells of the OMZ, denitrifiers may be as much
as 100-fold more abundant in the OMZ than outside it.
Along with the increase in cell number at later stages of
denitrification, we documented consistent changes in nirS
and nirK diversity. The pattern consists of high diversity of
denitrifying organisms in the initial stages of denitrification
and dominance by a few phylotypes after the intensification
of the process both in experimental incubations and under
natural (in situ) conditions. The in situ stations spanned the
environmental gradient representing the progression of
denitrification in both coastal and open-ocean waters
(Fig. 2b, c). These patterns are observed for both nirS and
nirK populations (Table 3, Fig. 2b, c). For both genes,
initially low nitrite concentration is associated with high
diversity of denitrifiers, while high nitrite concentration is
accompanied by low diversity. Independent evidence
(Figs. 3 and 4 and cited above) supports the correlation
between high nitrite/low diversity and high cell abundance.
In both the environment and in incubations, a bloom
occurs, but the particular organism that blooms varies in
both space and time.
The "bottle effect" is a familiar artifact that should be
suspected in interpreting the results from the long-term
incubations and their relevance to the natural environment.
Confinement, even in relatively large volume bottles (3 L),
can lead to changes in community composition in shallow
coastal waters [13]. Thus confinement alone could be
suspected in somehow enhancing the ability of the
assemblage to grow and denitrify even without nutrient
enrichment in the 10-L bags. Failure of the communities to
grow and denitrify in the ETNP and ETSP incubations in
the absence of nutrient additions, however, argues that
containment alone is not sufficient to induce changes in cell
number and DIN in OMZ water [50]. Similarly, long
periods of no growth or other response were also observed
for incubated samples from the Baltic Sea [5]. Denitrifica-
tion commenced only when additional carbon was added to
the incubations, which is consistent with our hypothesis
that episodic denitrification is driven by variable carbon
input from overlying waters. Thus, while the bag conditions
cannot be said to represent the natural environment, the
patterns of DIN and diversity changes parallel those
observed at similar stages of denitrification in the environ-
ment. Temporal variability in denitrification was hypothe-
sized to explain its apparent absence in waters where
anammox, but not denitrification, was easily detected by
15N incubation methods [46]. This might imply that
denitrification occurs in the environment in a batch
culture-like mode, when organic carbon is injected into
subsurface OMZ waters from localized or episodic blooms.
Implications of the Change in Community Structure
The bulk of nitrogen loss is expected to occur during the
mid to late stages (2 to 4) of denitrification. These stages
Denitrifying Bacterial Bloom Dynamics 359
Page 11
are recognized by their typical chemical signatures. The
SNM, which occurs in the region bounded by 12–22° N and
of nitrogen species. The largest nitrate deficit and greatest N2
excess occur within the SNM [12], as does the fastest
turnover of nitrous oxide [34, 35]. These hot spots support
the highest cell numbers but have the lowest denitrifier
diversity. Thus, the bulk of N loss in OMZs is likely to
occur when the denitrifying community is in a bloom-like
state, characterized by high biomass (e.g., Fig. 7), decreas-
ing diversity and increasing dominance (i.e., stages 2–5 in
Fig. 2). Because OMZs contribute disproportionately to the
global N loss, these few dominant OTUs, responding to the
pulsed organic matter supply to the OMZs, should be
responsible for a significant fraction of global nitrogen loss.
Just as nitrogen fixation in the surface ocean is thought to
be strongly influenced by low-diversity bloom events (e.g.,
the Trichodesmium blooms) [6], we suggest that subsurface,
low-diversity denitrification bloom events may also be
important in counter balancing the global N cycle.
Loreau et al. [26] pointed out that, because the bulk of
ecosystem processes are due to microorganisms, it is
important to understand the applicability of diversity–
function theory to microbial systems. Two theoretical
models, sampling effect and niche differentiation, offer
different explanations for the role of diversity in maximiz-
ing community and ecosystem function [48] and predict
different levels of diversity after succession under con-
ditions approaching equilibrium. The niche differentiation
model [49] predicts that multiple species will be maintained
as long as each has a competitive advantage due to a
resource, combination of resources, or environmental
conditions creating a niche where each species is a superior
competitor. In this case, maintaining high levels of diversity
leads to maximum function because habitat space can be
efficiently subdivided and biological diversity allows
optimization of this heterogeneity. In the sampling effect
model [1, 20, 49], the probability of including a dominant
competitor increases with diversity. A very diverse assem-
blage provides the background reservoir from which
environmental conditions can select the most "fit" biolog-
ical unit. Under stable conditions, this model predicts that
diversity will approach a monoculture of the dominant
competitor and function will increase towards an asymptote
equal to the functioning of that monoculture or blooming
microorganism. The fast growth of bacteria and relative
homogeneity of the water column environment may make
the sampling effect model more appropriate to describe the
importance of diversity over short time and small spatial
scales. The present data, in which OTU richness and
evenness decrease sharply with succession, are consistent
with the sampling effect. It has also been suggested that
diversity–function relationships should display less response
saturation when applied to highly dynamic populations such
as bacteria [42], allowing rapid functional optimization. At
a regional scale, the sampling effect model may be less
applicable. Although most late-stage denitrification samples
showed very low diversity and high dominance (Fig. 2)
consistent with the sampling effect, the dominant OTU was
variable in both space and time, consistent with the niche
differentiation model acting on larger spatial and temporal
scales. Therefore, high levels of landscape-level (gamma)
diversity are extremely important for providing the initial
reservoir of diversity on which selection can act to create
blooms that dominate ecosystem processes over the shorter
temporal and spatial scales. In the case of oceanic nitrogen
fixation and denitrification, these microbial blooms appear
to have a large role in the global fluxes.
Canonical Denitrification Versus Anammox
Denitrifier community dynamics documented here indicate
that nitrate deficits, and presumably removal of fixed
nitrogen, is associated with denitrifying bacteria in the
oxygen minimum zones, but the relative importance of
denitrifiers versus anammox bacteria in this removal process
remains unclear. Unlike both nirK and nirS type denitrifiers,
the phylogenetic composition of the anammox assemblage
did not vary among stations or stage of denitrification
(Table 3). Quantitative analysis, e.g., by quantitative PCR,
of these groups is a necessary next step in addressing the
question of their relative abundance.
Although denitrifying organisms are facultative anae-
robes that can denitrify at low oxygen concentrations [23],
in the Arabian Sea OMZ, vigorous denitrification, as inferred
a sharply defined threshold DO concentration of <1 μM
[29, 31]. The anaerobic ammonium oxidation process is also
reported to be reversibly inhibited at DO>1 μM [44],
but environmental incubations indicate that anammox toler-
ates and is active at much higher oxygen concentrations [25].
Denitrifiers, however, can switch to aerobic growth at high
oxygen concentrations, while anammox have no known
aerobic capabilities. Thus, sensitivity of the two types of
organisms to ambient DO levels may influence their survival
and distribution. The minimal reported doubling time for
anammox bacteria is about 11 days [44], while for
denitrifiers it is much less. Hence, in a system dominated
by episodic carbon input, denitrifiers appear to have an
advantage over anammox by virtue of their faster growth; the
computed doubling time for the microbial assemblage (based
on total cell counts) in our bag experiments ranged from 59
to 156 h [50]. The cell growth we observed in the bag
incubations could not have occurred for cells with a
generation time of 11 days. We detected diversity changes
for both nirS and nirK, and the latter was not present in the
360 A. Jayakumar et al.
Page 12
genome of uncultured anammox bacterium K. stuttgartien-
sis. Moreover, some depths within the open-ocean and
coastal OMZs are supersaturated with nitrous oxide [2].
Based on culture experiments and insights from the only
known anammox genome, K. stuttgartiensis, there is no
evidence that anammox is involved in N2O biogeochemistry
[45]. The correlation between high cell numbers, denitrifier
diversity patterns, and late-stage denitrification implies that
denitrifying bacteria dominate the biomass of the OMZ
when denitrification is occurring and that denitrifying
blooms are responsible for episodic high fixed N loss.
Quantification of denitrifier genes explicitly will be neces-
sary to test this hypothesis further.
Concluding Remarks and Speculations for Future Work
This study shows that diverse denitrifying assemblages are
common in OMZ waters and shows that diversity is
correlated with the stages of denitrification. The growth in
cell number [50] and decrease in diversity that are
characteristic of OMZs in active stages of denitrification
suggest that the removal of fixed nitrogen may occur via
episodically enhanced growth of denitrifying organisms in
the core of an OMZ. These hot spots are driven by the
episodic blooms of surface phytoplankton, which supply
organic matter flux to subsurface waters. The resulting
"blooms" of denitrifiers are analogous with N-fixing
blooms in surface waters and may even regulate N fixation
by controlling fixed N availability in upwelled surface
waters [10]. Although low-diversity events may be respon-
sible for the bulk of N loss, the dominant OTUs are variable
in space and time, suggesting that background microbial
diversity (landscape level diversity) provides a vital
reservoir from which selection can optimize the succes-
sional process to match environmental conditions. What
factors influence the dominance of one phylotype from the
more diverse regional gene pool remains to be investigated.
Increased capacity for rapid, pulse-driven growth combined
with tolerance of variable environmental conditions by
denitrifiers relative to anammox organisms, allows for
episodic denitrifier blooms that are responsible for large-
scale removal of fixed nitrogen and trace gas transforma-
tions. We suggest that low-diversity, bloom-forming,
microbial assemblages are a common feature of globally
important fluxes in the N cycle, including new production
by phytoplankton, N fixation in the surface water of the
ocean gyres, and also denitrification in subsurface oxygen
minimum zones.
Science Foundation grants to BBW and AJ. We thank Hema Naik
and P. V. Narvekar for the nutrient analyses and Caroline B. Tuit for
assistance with the bag incubations.
This work was supported by US National
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text:
BLACKSBURG, Va. — Virginia Tech added its first solar-powered bus shelter, which was installed on a Blacksburg Transit route, according to The Southwest Times.
The 12-foot shelter, purchased from Tolar Manufacturing Company Inc., is equipped with a solar light bar. A solar array re-charges the battery each day replacing energy that was used during the previous evening and includes a reserve to provide regular illumination even during raining or cloudy weather. For the full story, click here.
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Columna Albarino 2013
Columna - Galicia - Spain - Rias Baixas
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More than 200 students from the ACT have competed in the College Sevens at the University of Canberra on Wednesday, with the top two boys and girls teams set to advance to the next stage.
David Pocock will miss the rest of the 2014 Super Rugby season after undergoing a full reconstruction on his left knee, Wednesday night.
The ACT's Women's Sevens side will fight to keep its championship title this weekend when the national tournament heads to the AIS.
The ACT Under 20s are celebrating after eight players were selected for the Combined States team to contest the Australian Championships here in Canberra later this month.
The ACT's Junior Gold Cup squads have both made flying starts to their campaigns and will look forward to their next match against Hunter in Newcastle on Saturday.
With the Pacific Rugby Cup under way for another year, ACT rugby fans will be given plenty of opportunities to see some of the Pacific region's best talent on show in their own backyard.
The ACT XV has gone down narrowly to Argentina's B team, the Pampas, at RMC on Sunday afternoon in the second round of the Pacific Rugby Cup.
The University of Canberra Brumbies have claimed their first win of the 2014 Super Rugby season, defeating the Force 27-14 on their home soil to reclaim turf in the west.
The ACT 20s have come away from the national championships in Adelaide with a comprehensive, 96-7 win over the South Australians.
Robbie Coleman will make his first appearance in 2014 when the UC Brumbies travel to Perth to take on the Force this Saturday night.