Connecting biodiversity and biogeochemical role by microbial metagenomics

Abstract

The main objective of this PhD dissertation was to unveil the links between biogeochemistry and microbial diversity using metagenomics functional potential as a proxy to connect a mechanistic perspective with whole-system ecology. In order to explore the potential and limitations of metagenomics, two contrasted and widely studied lacustrine ecosystems with global ecological interest were selected. First, the Banyoles karstic system, a mirror to the past sulfurous and anoxic (euxinic) conditions where three lakes provide different euxinic situations where reduced compounds and sulfate were highly available: Lake Cisó, a small eutrophic lake with high carbon inputs, permanent anoxia and high euxinia; Lake Vilar, a meromictic mesotrophic lake; and Lake Banyoles basin CIII, a meromictic deep oligotrophic basin. And second, the ultraoligotrophic Lake Redon under three different limnological situations: the slush, an oxygenated environment with labile carbon from algal exudates; the epilimnion oxygenated layer with low availability of reduced compounds; and the hypolimnion, a dark layer under the influence of the mineralization microbial processes from the sediment. The previous knowledge on the biogeochemistry, ecology and functioning of these ecosystems, offered an excellent framework to connect the biodiversity and biogeochemical role by microbial metagenomics. The results showed higher bacterial novelty in the hypolimnia of euxinic lakes with Elusimicrobia and Chloroflexi harbouring the highest number of novel 16S rRNA gene sequences. The potential for dark carbon fixation in these lakes was tentatively assigned to Hydrogenophilales (Thiobacillus-like) and Gallionellales (Syderoxidans-like) via the Calvin cycle, Bacteroidales, Campylobacterales and Desulfarculales through the Arnon cycle, and Desulfobacterales via the reductive acetil-CoA cycle. If the findings from sulfurous lakes are equivalent to ancient oceans, Gallionellales may have played an important role in the biogeochemistry of the iron cycle, a low contribution of nitrification and archaea was probably accounting for the nitrogen cycle, Campylobacterales may have acted as the main players of denitrification, and Bacteroidales may have been main players for dissimilatory nitrate reduction to ammonium mainly in organic carbon-rich zones. The acquisition of laterally transferred genes offering new functional alternatives, was key in order to explain the ecological success of the recurrent green sulfur bacteria bloom in Lake Banyoles basin CIII. The drivers for such horizontal gene transfer were potentially phages. In the slush of the high-mountain Lake Redon, the community composition shift from winter to spring was characterized by a decrease in bacterial diversity, dominance of Bacteroidetes and consistent increases in bacterial abundance and production. The potential for nitrification in Lake Redon was mainly found in the slush and hypolimnion by ammonia-oxidizing bacteria. Lower abundances of nitrification genes were found in the epilimnion. Planktonic microbial communities of Lake Redon showed a higher genomic potential for assimilatory pathways (nitrite, phosphate and sulfate) than those from the Banyoles area. Overall, our analyses provide a new view on the well-known biogeochemical functioning of karstic and alpine lakes. Even with the limitations of metagenomics and annotation, we used the previous knowledge on the ecology of the lakes to prove that metagenomics is a very accurate way to unveil the links between functional potential and microbial biodiversity of any given ecosystem. We identified bacterial populations as potential key stone species of biogeochemical processes and provided new hypothesis to be further tested both through experimental approaches and detailed quantification of matter and energy fluxes.

L'objectiu principal d'aquesta tesi és explorar els vincles entre la biogeoquímica i la diversitat microbiana, mitjançant la metagenòmica com a eina per determinar el potencial funcional de les comunitats i connectar la perspectiva mecanicista amb l’holística en l'estudi dels ecosistemes. Per tal d'explorar el potencial i les limitacions de la metagenòmica, es van seleccionar dos ecosistemes lacustres contrastats i àmpliament estudiats amb interès ecològic global. En primer lloc, el sistema càrstic de Banyoles, un equivalent de les condicions sulfuroses i anòxiques (euxíniques) en l'inici de la vida a la Terra, seleccionant tres llacs que proporcionen diferents situacions limnològiques amb alta disponibilitat de compostos reduïts i sulfat: el Llac Cisó , un petit llac eutròfic amb importants entrades de carboni orgànic, anòxia permanent i alta euxinia; el Llac Vilar, un llac mesotròfic i meromíctic; i la cubeta CIII del llac Banyoles, una cubeta profunda, oligotròfica i meromíctica. I en segon lloc, l’ultraoligotròfic Llac Redon en tres situacions limnològiques diferents: les capes de granissat (slush), un ambient oxigenat amb carboni làbil procedent d’exsudats d'algues; la massa d'aigua oxigenada de l’epilímnion amb baixa disponibilitat de compostos reduïts; i l'hipolímnion, una massa d'aigua en foscor sota la influència de processos microbians de mineralització que es donen en el sediment. El coneixement previ de la biogeoquímica, ecologia i funcionament d'aquests ecosistemes, ha ofert un excel·lent marc per a establir els vincles entre biodiversitat microbiana i funció biogeoquímica mitjançant una aproximació metagenòmica. En conjunt, aquesta tesi proporciona una nova visió sobre el funcionament biogeoquímic de llacs càrstics i alpins. Tot i les limitacions intrínseques a la metagenòmica i al procés d'anotació gènica, hem utilitzat els coneixements previs sobre l'ecologia dels llacs per demostrar que la metagenòmica és una eina molt precisa per donar a conèixer els vincles entre el potencial funcional i la biodiversitat microbiana de qualsevol ecosistema. S'han identificat les poblacions bacterianes potencialment responsables dels processos biogeoquímics i es proporcionen noves hipòtesis que hauran de ser comprovades mitjançant enfocaments experimentals i de quantificació dels fluxos de matèria i energia implicats.