A study published in Nature Communications reveals the impact of the environment on the genetic adaptation of bacteria. Environments rich in nutrients favor those that have evolved by losing genes involved in metabolic processes such as the self-production of amino acids. Streamlining the genome represents a significant energy saving, giving them an advantage in contexts where these nutrients are readily available.
In the scientific article, researchers from the Universities of Colorado, Aalborg, the Lawrence Berkeley Lab, and the Advanced Studies Center of Blanes (CEAB-CSIC) unveil crucial connections between the environment, survival strategies, and the genetic evolution of bacteria.
To achieve this, the team analyzed information stored in over 26,000 bacterial genomes and 3,800 metagenomes from natural environments such as soils, oceans, lakes, water treatment plants, human and plant microbiotas, as well as foods like sourdough or cheese, using supercomputing. The goal was to correlate genes, survival strategies, and the environment to determine conditions favouring the loss of genes related to amino acid production and the consequent energy saving for survival.
The study reveals that the majority of bacteria—80%, a higher percentage than previously believed—can produce the necessary amino acids for their functioning on their own. The remaining 20% cannot and depend on interaction with other living organisms or with the environment. Similar to humans, this second type of microorganism is obliged to obtain essential compounds through the diet, and they are called “auxotrophs.”
The research highlights that auxotrophic bacteria thrive in environments rich in amino acids, such as human intestines or foods like dairy products. In these nutrient-rich environments, there is a tendency for the evolution towards the loss of genes responsible for amino acid production.
Josep Ramoneda, the lead author of the article, explains the reason simply: “Why make an effort when everything is within reach? Having constant access to a ‘free buffet’ makes self-production of amino acids no longer an advantage. These environments have favored a genome optimization strategy in which bacteria have eliminated unnecessary genes. This has helped them minimize energy costs and thrive. A radical example are mycoplasmas, implicated in numerous diseases, which obtain amino acids from the cells of the humans they parasitize.“
The researchers also found that those bacteria depending on external supply have significantly smaller genomes than those that are self-sufficient, and are lacking genes for other metabolisms like those for sugars or lipids. This suggests that the loss of genes related to amino acid production is just one part of a broader genome rationalization strategy.
The work demonstrates that genomic optimization, due to the significant energy savings it entails, can be a winning strategy in nutrient-rich ecosystems. It also highlights that, in most environments, especially those lacking nutrients, self-sufficiency remains the best option.
Emilio O. Casamayor, a researcher at CEAB-CSIC and co-author of the study, points out that “in aquatic environments, where finding food is more challenging or intermittent, such as in high mountain lakes or the ocean, we have shown that genome rationalization is not the successful strategy. These environments favour bacteria that are self-sufficient.” He adds that “research like this is possible thanks to the combination of massive sequencing and computing techniques, allowing us to tackle more predictive ecological studies in the microbial world on large scales, approaches that were obscured until recently.”
The researchers urge further exploration of the relationship between the environment and the evolutionary adaptation of microbes to advance our understanding of microbial life through increasingly predictive approaches.
Utafiti uliochapishwa katika Nature Communications unafunua athari za mazingira juu ya marekebisho ya maumbile ya bakteria. Mazingira yenye virutubisho vingi hufaidika na yale ambayo yamebadilika kwa kupoteza jeni zinazohusika katika michakato ya kimetaboliki kama vile uzalishaji wa amino asidi. Kuimarisha genome inawakilisha akiba kubwa ya nishati, kuwapa faida katika muktadha ambapo virutubisho hivi ni inapatikana kwa urahisi. Katika makala ya kisayansi, watafiti kutoka Chuo Kikuu cha Colorado, Aalborg, Lawrence Berkeley Lab, na Kituo cha Mafunzo ya Juu cha Blanes (CEAB-CSIC) wanafunua uhusiano muhimu kati ya mazingira, mikakati ya kuishi, na mageuzi ya maumbile ya bakteria. Kwa mujibu wa utafiti huo, wataalamu hao walichunguza habari zilizomo katika genomes zaidi ya 26,000 za bakteria na metagenomes 3,800 kutoka mazingira ya asili kama vile udongo, bahari, maziwa, vituo vya kusafisha maji, microbiomes ya binadamu na mimea, na pia vyakula kama vile sourdough au jibini. Lengo lilikuwa kuunganisha jeni, mikakati ya kuishi, na mazingira ili kuamua hali zinazopendelea upotezaji wa jeni zinazohusiana na uzalishaji wa asidi ya amino na uhifadhi wa nishati unaotokana na kuishi. Utafiti huo unaonyesha kwamba bakteria nyingi - asilimia 80 - asilimia kubwa kuliko ilivyodhaniwa hapo awali - zinaweza kutengeneza asidi za amino zinazohitajika kwa utendaji wao wenyewe. Asilimia 20 ya viumbe hai huishi na kuingiliana na viumbe wengine au mazingira. "Kama ilivyo kwa wanadamu, aina hii ya pili ya viumbe wadogo ni wajibu wa kupata misombo muhimu kupitia mlo, na wao ni kuitwa ""auxotrophs.""Utafiti unaonyesha kwamba bakteria auxotrophs kusitawi katika mazingira tajiri katika amino asidi, kama vile matumbo ya binadamu au vyakula kama bidhaa za maziwa." Katika mazingira haya yenye virutubisho vingi, kuna mwelekeo wa mageuzi kuelekea kupoteza jeni zinazohusika na uzalishaji wa asidi ya amino. Ramon Josepeda, mwandishi mkuu wa makala hiyo, anaeleza sababu hiyo kwa urahisi: <unk>Kwa nini ujitahidi wakati kila kitu kiko karibu? Kuwa na upatikanaji wa daima wa "buffet ya bure" hufanya uzalishaji wa amino asidi ya kibinafsi usiwe na faida. Mazingira hayo yamependelea mbinu ya kuboresha chembe za urithi ambazo bakteria zimeondoa chembe zisizohitajika. Hilo limewasaidia kupunguza gharama za nishati na kusitawi. Mifano ya msingi ni mycoplasmas, zinazohusika katika magonjwa mengi, ambazo hupata amino asidi kutoka kwa seli za wanadamu wanaowachukia. <unk> Watafiti pia waligundua kuwa bakteria hizo zinazotegemea usambazaji wa nje zina genomes ndogo sana kuliko zile ambazo zinajitosheleza, na hazina jeni kwa metabolisms zingine kama zile za sukari au lipids. Hii inaonyesha kwamba kupoteza jeni zinazohusiana na uzalishaji wa asidi ya amino ni sehemu moja tu ya mkakati mkubwa wa usawa wa genome. Kazi inaonyesha kwamba genomic optimization, kutokana na kuokoa nishati kubwa inahusisha, inaweza kuwa mkakati kushinda katika mazingira tajiri ya virutubisho. Pia inasisitiza kwamba, katika mazingira mengi, hasa yale yanayokosa virutubisho, kujitegemea bado ni chaguo bora. Emilio O. Casamayor, mtafiti wa CEAB-CSIC na mwandishi mwenza wa utafiti huo, anasema kuwa katika mazingira ya majini, ambapo kupata chakula ni changamoto zaidi au mara kwa mara, kama vile katika maziwa ya mlima wa juu au bahari, tumeonyesha kuwa uhalali wa genome sio mkakati wa mafanikio. "Kama ilivyoelezwa hapo juu, utafiti kama huu unawezekana kwa sababu ya mchanganyiko wa utaratibu mkubwa na mbinu za kompyuta, ambazo zinaturuhusu kushughulikia masomo zaidi ya ikolojia ya utabiri katika ulimwengu wa vimelea kwa kiwango kikubwa, mbinu ambazo zilikuwa zimefichwa hadi hivi karibuni. ""Watafiti wanahimiza uchunguzi zaidi wa uhusiano kati ya mazingira na marekebisho ya magonjwa ili kuendeleza uelewa wetu wa maisha ya vimelea."