Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics

Abstract

Stratified sulfurous lakes are appropriate environments for studying the links between composition and functionality in microbial communities and are potentially modern analogs of anoxic conditions prevailing in the ancient ocean. We explored these aspects in the Lake Banyoles karstic area (NE Spain) through metagenomics and in silico reconstruction of carbon, nitrogen and sulfur metabolic pathways that were tightly coupled through a few bacterial groups. The potential for nitrogen fixation and denitrification was detected in both autotrophs and heterotrophs, with a major role for nitrogen and carbon fixations in Chlorobiaceae. Campylobacterales accounted for a large percentage of denitrification genes, while Gallionellales were putatively involved in denitrification, iron oxidation and carbon fixation and may have a major role in the biogeochemistry of the iron cycle. Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium. The very low abundance of genes for nitrification, the minor presence of anammox genes, the high potential for nitrogen fixation and mineralization and the potential for chemotrophic CO2 fixation and CO oxidation all provide potential clues on the anoxic zones functioning. We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments. Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems.

The environmental and host‐associated bacterial microbiota of Arctic seawater‐farmed Atlantic salmon with ulcerative disorders

“…Campylobacterales and other Epsilonproteobacteria are frequently detected in marine systems where they are coupled to denitrification (Llorens‐Mares et al . ; Fortunato & Huber ). Desulfobacterales with reads clustering to Desulfobulbaceae and Desulfobacteraceae are known sulphate reducers that benefit from organic enriched sediments of marine fish farms (Kondo et al .…”

Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community

“…Venn diagrams were computed by analysing the 100% complete kegg pathway modules for the three most dominant phyla. Marker genes for the analysis of the carbon, nitrogen and sulphur metabolism were selected and analysed as described by the Llorens‐Mares and colleagues ().…”

Geomicrobiology of the carbon, nitrogen and sulphur cycles in Powell Lake: a permanently stratified water column containing ancient seawater

“…A universal microbiome for meromictic lakes likely does not exist, given the geographical, geochemical and physical diversity between different meromictic lakes, but some commonly occurring taxonomic groups can be identified. These include Cyanobacteria , Alphaproteobacteria , Actinobacteria and Verrucomicrobia (mostly in the oxic surface and oxycline), Chlorobi , Beta ‐ and Gammaproteobacteria (mostly in the chemocline), Bacteroidetes (throughout) as well as Deltaproteobacteria , candidate phyla (particularly Omnitrophica , Atribacteria , Microgenomates ) and Chloroflexi in the anoxic monimolimnion (Lehours et al ., ; Lauro et al ., ; Comeau et al ., ; Klepac‐Ceraj et al ., ; Gies et al ., ; Llorens‐Marès et al ., ; İnceoğlu et al ., ; Baatar et al ., ). Anoxygenic photoautotrophy by green ( Chlorobi ) or purple ( Chromatiales ) sulphur bacteria and also chemolithoautotrophy are typical processes in meromictic water columns (Cloern et al ., ; Overmann and Tilzer, ; Overmann et al ., ; Casamayor et al ., ; Zadereev et al ., ).…”

“…Anoxygenic photoautotrophy by green ( Chlorobi ) or purple ( Chromatiales ) sulphur bacteria and also chemolithoautotrophy are typical processes in meromictic water columns (Cloern et al ., ; Overmann and Tilzer, ; Overmann et al ., ; Casamayor et al ., ; Zadereev et al ., ). Thaumarchaeota and Betaproteobacteria (ammonium oxidation), Nitrospirae (nitrite oxidation), Gammaproteobacteria (methanotrophy), Betaproteobacteria , Chromatiales and Chlorobi (sulphide oxidation) have been linked to the processes that oxidize the inorganic reductants that diffuse upwards into the chemoclines and oxyclines of meromictic lakes (Pouliot et al ., ; Crowe et al ., ; Llorens‐Marès et al ., ; İnceoğlu et al ., ; Baatar et al ., ; Oswald et al ., ).…”