Single-cell genomics-based analysis reveals a vital ecological role of Thiocapsa sp. LSW in the meromictic Lake Shunet, Siberia

Meromictic lakes usually harbour certain prevailing anoxygenic phototrophic bacteria in their anoxic zone, such as the purple sulfur bacterium (PSB) Thiocapsa sp. LSW (hereafter LSW) in Lake Shunet, Siberia. PSBs have been suggested to play a vital role in carbon, nitrogen and sulfur cycling at the oxic–anoxic interface of stratified lakes; however, the ecological significance of PSBs in the lake remains poorly understood. In this study, we explored the potential ecological role of LSW using a deep-sequencing analysis of single-cell genomics associated with flow cytometry. An approximately 2.7 Mb draft genome was obtained based on the co-assembly of five single-cell genomes. LSW might grow photolithoautotrophically and could play putative roles not only as a carbon fixer and diazotroph, but also as a sulfate reducer/oxidizer in the lake. This study provides insights into the potential ecological role of Thiocapsa sp. in meromictic lakes.

Metagenomic Insights Into Ecosystem Function in the Microbial Mats of a Large Hypersaline Coastal Lagoon System

The hypersaline lagoon system of Araruama (HLSA) is one of the largest in the world and one of the most important sources of evaporative salt in Brazil. The biogeochemical characteristics of this lagoon system led it to be considered a Precambrian relic. The HLSA also harbors extensive microbial mats, but the taxonomic and metabolic attributes of these mats are poorly understood. Our high-throughput metagenomics analyses demonstrated that the HLSA microbial mats are dominated by Proteobacteria, Cyanobacteria, and Bacteroidetes. Among Proteobacteria, Deltaproteobacteria comprises approximately 40% of the total population and it includes sulfate-reducing bacteria such as Desulfobacterales, Desulfuromonadales, and Desulfovibrionales. Differing in composition and function of their reaction centers, other phylogenetic diverse anoxygenic phototrophic bacteria were detected in the HLSA microbial mats metagenomes. The presence of photolithoautotrophs, sulfate reducers, sulfide oxidizers, and aerobic heterotrophs suggests the existence of numerous cooperative niches that are coupled and regulated by microbial interactions. We suggest that the HLSA microbial mats hold microorganisms and the necessary machinery (genomic repertoire to sustain metabolic pathways) to promote favorable conditions (i.e., create an alkaline pH microenvironment) for microbially mediated calcium carbonate precipitation process. Metagenome-assembled genomes (Ca. Thiohalocapsa araruaensis HLSAbin6 sp. nov. and Ca. Araruabacter turfae HLSAbin9 gen. nov. sp. nov.) obtained support the relevance of Sulfur metabolism and they are enriched with genes involved in the osmoadaptive networks, hinting at possible strategies to withstand osmotic stress. Metabolically versatile bacteria populations, able to use multiple nutrient sources and osmolytes, seem to be a relevant attribute to survive under such stressful conditions.

“Candidatus Chlorobium masyuteum,” a Novel Photoferrotrophic Green Sulfur Bacterium Enriched From a Ferruginous Meromictic Lake

Anoxygenic phototrophic bacteria can be important primary producers in some meromictic lakes. Green sulfur bacteria (GSB) have been detected in ferruginous lakes, with some evidence that they are photosynthesizing using Fe(II) as an electron donor (i.e., photoferrotrophy). However, some photoferrotrophic GSB can also utilize reduced sulfur compounds, complicating the interpretation of Fe-dependent photosynthetic primary productivity. An enrichment (BLA1) from meromictic ferruginous Brownie Lake, Minnesota, United States, contains an Fe(II)-oxidizing GSB and a metabolically flexible putative Fe(III)-reducing anaerobe. “Candidatus Chlorobium masyuteum” grows photoautotrophically with Fe(II) and possesses the putative Fe(II) oxidase-encoding cyc2 gene also known from oxygen-dependent Fe(II)-oxidizing bacteria. It lacks genes for oxidation of reduced sulfur compounds. Its genome encodes for hydrogenases and a reverse TCA cycle that may allow it to utilize H2 and acetate as electron donors, an inference supported by the abundance of this organism when the enrichment was supplied by these substrates and light. The anaerobe “Candidatus Pseudopelobacter ferreus” is in low abundance (∼1%) in BLA1 and is a putative Fe(III)-reducing bacterium from the Geobacterales ord. nov. While “Ca. C. masyuteum” is closely related to the photoferrotrophs C. ferroooxidans strain KoFox and C. phaeoferrooxidans strain KB01, it is unique at the genomic level. The main light-harvesting molecule was identified as bacteriochlorophyll c with accessory carotenoids of the chlorobactene series. BLA1 optimally oxidizes Fe(II) at a pH of 6.8, and the rate of Fe(II) oxidation was 0.63 ± 0.069 mmol day–1, comparable to other photoferrotrophic GSB cultures or enrichments. Investigation of BLA1 expands the genetic basis for phototrophic Fe(II) oxidation by GSB and highlights the role these organisms may play in Fe(II) oxidation and carbon cycling in ferruginous lakes.

An Aerobic Anoxygenic Phototrophic Bacterium Fixes CO2 via the Calvin-Benson-Bassham Cycle

Aerobic anoxygenic phototrophic bacteria (AAnPB) are photoheterotrophs, which use light as auxiliary energy and require organic carbon (OC) for growth. Herein, we report the unusual strain B3, which is a true AAnPB because it requires oxygen for growth, harbours genes for cbb3- and bd-type cytochromes and acsF, and produces bacteriochlorophyll. The B3 genome encodes the complete metabolic pathways for AAnPB light utilization, CO2 fixation via Calvin-Benson-Bassham (CBB) cycle and oxidation of sulfite and H2, and the transcriptome indicated that all components of these pathways were fully transcribed. Expression of the marker genes related to photosynthesis, including pufM for light harnessing and rbcL for CO2 fixation, and the activity of RubisCO, the key enzyme in the Calvin-Benson-Bassham (CBB) cycle, increased in response to decreased OC supply. Large amounts of cell biomass were obtained in liquid BG11 medium under illumination. The strain thus likely photoautotrophically grows using sulfite or H2 as an electron donor. Similar GC contents between photosynthesis, the CBB cycle and 16S rRNA genes and the consistency of their phylogenetic topologies implied that light harnessing and carbon fixation genes evolved vertically from an anaerobic phototrophic ancestor of Rhodospirillaceae in Alphaproteobacteria. In conclusion, strain B3 represents a novel AAnPB characterized by photoautotrophy using the CBB cycle. This kind of AAnPB may be ecologically significant in the global carbon cycle.

The role of anoxygenic phototrophs in the Baltic Sea

<p>Both oxygenic and anoxygenic phototrophic bacteria (OPB and APB, respectively) are widely distributed in the ocean and play significant roles in carbon cycle and marine productivity. These organisms capture light as energy source via chlorophyll or bacteriochlorophylls-based photosystems. While OPB are relatively well studied, information on APB is rather scarce although they have been shown abundant in some ocean ecosystems and may play an important role in oxygen depleted environments. Here, we investigate the spatial profile of OPB and APB, gene abundance and expression of the key functional marker gene <em>pufM </em>(APB specific photosynthetic reaction center subunit M), in one fjord and three basins of the Baltic Sea using 16S rRNA amplicon sequencing and qPCR. Among the microbial community, abundances of OPB and APB were found to be similar thus emphasizing a potential importance of APB, with APB representing 1.6-17.5% and OPB representing 0.5-20%. Among APB, we identified eleven different orders, with <em>Rhodobacterales</em> being quantitatively dominant. The identified seven orders of OPB were dominated by <em>Synechococcales</em>. OPB were more abundant than APB in surface waters (<8m), while APB were comparably more abundant in deeper waters. Besides a depth-dependent distribution, we observed an impact of salinity on the distribution of APB and OPB, both of which being suggestive of distinct niches for those primary producer clades. <em>pufM</em> gene abundance ranged from 10<sup>4</sup> to 10<sup>9</sup> copies/L, with highest counts detectable in the mixed layer (<40m), however, even in deeper waters where gene abundances decreased APB <em>pufM</em> gene expression was high with up to 10<sup>4</sup> copies/L. These results indicate APB may play a more important role in marine primary productivity which has been underestimated before. </p>