Beyond the Calvin cycle: autotrophic carbon fixation in the ocean

Genome assembly of the chemosynthetic endosymbiont of the hydrothermal vent snail Alviniconcha adamantis from the Mariana Arc

Chemosynthetic animal-microbe symbioses sustain hydrothermal vent communities in the global deep sea. In the Indo-Pacific Ocean, hydrothermal ecosystems are often dominated by gastropod species of the genus Alviniconcha, which live in association with chemosynthetic Gammaproteobacteria or Campylobacteria. While the symbiont genomes of most extant Alviniconcha species have been sequenced, no genome information is currently available for the gammaproteobacterial endosymbiont of Alviniconcha adamantis—a comparatively shallow living species that is thought to be the ancestor to all other present Alviniconcha lineages. Here, we report the first genome sequence for the symbiont of A. adamantis from the Chamorro Seamount at the Mariana Arc. Our phylogenomic analyses show that the A. adamantis symbiont is most closely related to Chromatiaceae endosymbionts of the hydrothermal vent snails Alviniconcha strummeri and Chrysomallon squamiferum, but represents a distinct bacterial species or possibly genus. Overall, the functional capacity of the A. adamantis symbiont appeared to be similar to other chemosynthetic Gammaproteobacteria, though several flagella and chemotaxis genes were detected, which are absent in other gammaproteobacterial Alviniconcha symbionts. These differences might suggest potential contrasts in symbiont transmission dynamics, host recognition, or nutrient transfer. Furthermore, an abundance of genes for ammonia transport and urea usage could indicate adaptations to the oligotrophic waters of the Mariana region, possibly via recycling of host- and environment-derived nitrogenous waste products. This genome assembly adds to the growing genomic resources for chemosynthetic bacteria from hydrothermal vents and will be valuable for future comparative genomic analyses assessing gene content evolution in relation to environment and symbiotic lifestyles.

Unexpected diversity found within benthic microbial mats at hydrothermal springs in Crater Lake, Oregon

Crater Lake, Oregon is an oligotrophic freshwater caldera lake fed by thermally and chemically enriched hydrothermal springs. These vents distinguish Crater Lake from other freshwater systems and provide a unique ecosystem for study. This study examines the community structure of benthic microbial mats occurring with Crater Lake hydrothermal springs. Small subunit rRNA gene amplicon sequencing from eight bacterial mats was used to assess community structure. These revealed a relatively homogeneous, yet diverse bacterial community. High alpha diversity and low beta diversity indicate that these communities are likely fueled by homogeneous hydrothermal fluids. An examination of autotrophic taxa abundance indicates the potential importance of iron and sulfur inputs to the primary productivity of these mats. Chemoautotrophic potential within the mats was dominated by iron oxidation from Gallionella and Mariprofundus and by sulfur oxidation from Sulfuricurvum and Thiobacillus with an additional contribution of nitrite oxidation from Nitrospira. Metagenomic analysis showed that cbbM genes were identified as Gallionella and that aclB genes were identified as Nitrospira, further supporting these taxa as autotrophic drivers of the community. The detection of several taxa containing arsC and nirK genes suggests that arsenic detoxification and denitrification processes are likely co-occurring in addition to at least two modes of carbon fixation. These data link the importance of the detected autotrophic metabolisms driven by fluids derived from benthic hydrothermal springs to Crater Lake’s entire lentic ecosystem.

Effects of agricultural land use on the differentiation of nitrifier communities and functional patterns from natural terrestrial ecosystems

Human activities severely affect the global nitrogen (N) cycle. Croplands receive intensive N fertilization; consequently, cropland and natural ecosystem differentiation often results in community and functional variation in N-transforming microbes, including nitrifiers, which perform nitrification central to N cycle. However, evidence of such variation is mostly limited to ammonia oxidizers (AO) in local fields, excluding soil heterogeneity and nitrite-oxidizing bacteria (NOB); the variation under diverse climatic and soil conditions is not comprehensively understood. We conducted a large-scale survey of 131 cropland and natural sites in China. The community patterns of ammonia-oxidizing bacteria (AOB) and NOB differed significantly between croplands and some natural ecosystems, whereas ammonia-oxidizing archaea (AOA) were not affected by ecosystem type. The AOB population and nitrification potential (NP) were significantly higher in agroecosystems than in natural systems except wetlands. Fewer co-occurrence interactions involving nitrifiers were observed in croplands than in natural ecosystems except forests, systematically indicating the ecological diversification of nitrifiers in potential microbial associations among these habitats. Ecosystem type, pH, organic matter (OM), total phosphorus (TP), mean annual temperature (MAT) and mean annual precipitation (MAP) were primary drivers of nitrifier community and functional shifts. This study provides the first large-scale evidence of overall nitrifier community (i.e., AOA, AOB and NOB) and potential functional shifts between agroecosystems and natural environments, enabling predictions of terrestrial N cycle under foreseeable natural land use conversions and global climate change.

Community characteristics of autotrophic CO2-fixing bacteria in karst wetland groundwaters with different nitrogen levels

Karst wetlands are important in the global carbon and nitrogen cycles as well as in security of water resources. Huixian wetland (Guilin) is the largest natural karst wetland in China. In recent years, groundwater nitrogen pollution has increasingly affected the wetland ecosystem integrity due to anthropogenic activities. In this study, it was hypothesized that autotrophic microbial diversity is impacted with the advent of pollution, adversely affecting autotrophs in the carbon and nitrogen cycles. Autotrophic microbes have important roles in abating groundwater nitrogen pollution. Thus, it is of great significance to study the characteristics of autotrophic bacterial communities and their responses to environmental parameters in nitrogen-polluted karst groundwaters. The abundances of the Calvin-Benson cycle functional genes cbbL and cbbM as well as the autotrophic CO2-fixing bacterial communities were characterized in the karst groundwater samples with different levels of nitrogen pollution. The cbbM gene was generally more abundant than the cbbL gene in the groundwater samples. The cbbL gene abundance was significantly positively correlated with dissolved inorganic nitrogen (DIN) concentration (P < 0.01). In the autotrophic CO2-fixing bacterial communities, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria of the phylum Proteobacteria were predominant. At the genus level, Rubrivivax and Methylibium were the dominant cbbL gene containing genera, while Halothiobacillus and Endothiovibrio were the dominant genera for the cbbM gene. The abundance of autotrophic CO2-fixing bacterial communities increased but their diversity decreased with the inflow of nitrogen into the karst groundwater system. The community structure of autotrophic CO2-fixing bacteria in the groundwaters was also significantly affected by environmental factors such as the carbonic anhydrase (CA) activity, dissolved inorganic carbon (DIC) concentration, temperature, and oxidation-reduction potential (ORP). Nitrogen inflow significantly changed the characteristics of autotrophic CO2-fixing bacterial communities in the karst groundwaters. Some key genera such as Nitrosospira and Thiobacillus were clearly abundant in the karst groundwaters with high nitrogen levels. Their respective roles in nitrification and denitrification impact nitrogen removal in this ecosystem. The findings in this study provide an important reference for biological abatement of nitrogen pollution in the karst groundwater system.

Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts

Shrimps of the family Alvinocarididae, endemic species to deep sea chemosynthetic ecosystems, harbor epibiotic microbes on gills which probably play important roles in the survival of the shrimps. Among them, Alvinocaris longirostris and Shinkaicaris leurokolos occupy different ecological niches within the same hydrothermal vent in Okinawa Trough, and A. longirostris also exists in a methane seep of the South China Sea. In this study, full-length 16S rRNA sequences of the gill associated bacteria of two alvinocaridid species from different chemosynthetically ecological niches were first captured by single-molecule real-time sequencing. Totally, 120,792 optimized circular consensus sequences with ∼1,450 bp in length were obtained and clustered into 578 operational taxonomic units. Alpha diversity analysis showed seep A. longirostris had the highest species richness and evenness (average Chao1 = 213.68, Shannon = 3.39). Beta diversity analysis revealed that all samples were clearly divided into three groups, and microbial community of A. longirostris from seep and vent were more related than the other comparisons. By permutational multivariate analysis of variance, the most significant community compositional variance was detected between seep A. longirostris and vent S. leurokolos (R ² = 0.731, P = 0.001). The taxon tags were further classified into 21 phyla, 40 classes, 89 orders, 124 families and 135 genera. Overall, the microbial communities were dominated by Campylobacteria and Gammaproteobacteria. Alphaproteobacteria, Bacteroidia, Verrucomicrobiae, Bacilli and other minor groups were also detected at lower abundance. Taxonomic groups recovered from the vent S. leurokolos samples were only dominated by Sulfurovaceae (94.06%). In comparison, gill-associated microbiota of vent A. longirostris consisted of more diverse sulfur-oxidizing bacteria, including Sulfurovaceae (69.21%), Thiotrichaceae (6.77%) and a putative novel Gammaproteobacteria group (14.37%), while in seep A. longirostris, Gammaproteobacteria un-group (44.01%) constituted the major component, following the methane-oxidizing bacteria Methylomonadaceae (19.38%), and Sulfurovaceae (18.66%). Therefore, the gill associated bacteria composition and abundance of alvinocaridid shrimps are closely related to the habitat heterogeneity and the selection of microbiota by the host. However, the interaction between these alvinocaridid shrimps and the epibiotic communities requires further study based on metagenome sequencing and fluorescence in situ hybridization.

The transcriptional regulator RbcR controls ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) genes in the cyanobacterium Synechocystis sp. PCC 6803

Oxygenic photosynthesis evolved in cyanobacteria, primary producers of striking ecological importance. Like plants, cyanobacteria use the Calvin-Benson-Bassham cycle for CO₂ fixation, fuelled by ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). In a competitive reaction this enzyme also fixes O₂ which makes it rather ineffective. To mitigate this problem, cyanobacteria evolved a CO₂ concentrating mechanism (CCM) to pool CO₂ in the vicinity of RuBisCO. However, the regulation of these carbon (C) assimilatory systems is understood only partially. Using the model Synechocystis sp. PCC 6803 we characterized an essential LysR-type transcriptional regulator encoded by gene sll0998. Transcript profiling of a knockdown mutant revealed diminished expression of several genes involved in C acquisition, including rbcLXS, sbtA and ccmKL encoding RuBisCO and parts of the CCM, respectively. We demonstrate that the Sll0998 protein binds the rbcL promoter and acts as a RuBisCO regulator (RbcR). We propose ATTA(G/A)-N₅ -(C/T)TAAT as the binding motif consensus. Our data validate RbcR as a regulator of inorganic C assimilation and define the regulon controlled by it. Biological CO₂ fixation can sustain efforts to reduce its atmospheric concentrations and is fundamental for the light-driven production of chemicals directly from CO₂ . Information about the involved regulatory and physiological processes is crucial to engineer cyanobacterial cell factories.

Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways

BACKGROUND

Autotrophic carbon fixation is the primary route through which organic carbon enters the biosphere, and it is a key step in the biogeochemical carbon cycle. The Calvin-Benson-Bassham pathway, which is predominantly found in plants, algae, and some bacteria (mainly cyanobacteria), was previously considered to be the sole carbon-fixation pathway. However, the discovery of a new carbon-fixation pathway in sulfurous green bacteria almost two decades ago encouraged further research on previously overlooked ancient carbon-fixation pathways in taxonomically and phylogenetically distinct microorganisms.

AIM OF REVIEW

In this review, we summarize the six known natural carbon-fixation pathways and outline the newly proposed additions to this list. We also discuss the recent achievements in synthetic carbon fixation and the importance of the metabolism of thermophilic microorganisms in this field.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Currently, at least six carbon-fixation routes have been confirmed in Bacteria and Archaea. Other possible candidate routes have also been suggested on the basis of emerging "omics" data analyses, expanding our knowledge and stimulating discussions on the importance of these pathways in the way organisms acquire carbon. Notably, the currently known natural fixation routes cannot balance the excessive anthropogenic carbon emissions in a highly unbalanced global carbon cycle. Therefore, significant efforts have also been made to improve the existing carbon-fixation pathways and/or design new efficient in vitro and in vivo synthetic pathways.

Composition and Ecological Roles of the Core Microbiome along the Abyssal-Hadal Transition Zone Sediments of the Mariana Trench

The unique geological features of hadal trenches are known to influence both the structure and ecological function of microbial communities. It is also well known that heterotrophs and chemoautotrophs dominate the hadal and abyssal pelagic zones, respectively. Here, a metagenomic investigation was conducted on sediment samples obtained from the abyssal-hadal transition zone in the Mariana Trench to gain a better understanding of the general diversity and potential function of the core microbiome in this zone. A high level of cosmopolitanism existed in the core microbiome referred from a high community similarity among different stations. Niche differentiation along the fine-scale of different sediment layers was observed, especially for major archaeal groups, largely due to sediment depth and the source of organic matter. A prevalence of nitrogen biogeochemical cycles driven by various nitrifying groups with the capability of dark carbon fixation in the abyssal-hadal biosphere was also demonstrated. The predominance of heterotrophic over chemolithoautotrophic pathways in this transition zone was found, and a high abundance of genes related to respiration and carbon fixation (i.e., the intact Calvin and rTCA cycles) were detected as well, which might reflect the intensive microbial activities known to occur in this deep biosphere. The presence of those metabolic processes and associated microbes were reflected by functional and genetic markers generated from the metagenomic data in the current study. However, their roles and contributions to the nitrogen/carbon biogeochemical cycles and flux in the abyssal-hadal transition zone still need further analysis. IMPORTANCE The Mariana Trench is the deepest oceanic region on earth, its microbial ecological exploration has become feasible with the rapid progress of submersible and metagenomic sequencing. We investigated the community compositions and metabolic functions of the core microbiome along the abyssal-hadal transition zone of the Mariana Trench, although most studies by far were focused on the pelagic zone. We found a predominance of heterotrophic groups and related metabolic pathways, which were closely associated with nitrogen biogeochemical cycles driven by various nitrifying groups with the capability of dark carbon fixation.

Lipid Profiles From Fresh Biofilms Along a Temperature Gradient on a Hydrothermal Stream at El Tatio (Chilean Andes), as a Proxy for the Interpretation of Past and Present Biomarkers Beyond Earth

Hydrothermal systems and their deposits are primary targets in the search for fossil evidence of life beyond Earth. However, to learn how to decode fossil biomarker records in ancient hydrothermal deposits, we must first be able to interpret unambiguously modern biosignatures, their distribution patterns, and their association with physicochemical factors. Here, we investigated the molecular and isotopic profile of microbial biomarkers along a thermal gradient (from 29 to 72°C) in a hot spring (labeled Cacao) from El Tatio, a geyser field in the Chilean Andes with abundant opaline silica deposits resembling the nodular and digitate structures discovered on Mars. As a molecular forensic approach, we focused on the analysis of lipid compounds bearing recognized resistance to degradation and the potential to reconstruct the paleobiology of an environment on a broader temporal scale than other, more labile, biomolecules. By exploiting the lipid biomarkers’ potential to diagnose biological sources and carbon fixation pathways, we reconstructed the microbial community structure and its ecology along the Cacao hydrothermal transect. The taxonomic adscription of the lipid biomarkers was qualitatively corroborated with DNA sequencing analysis. The forensic capacity of the lipid biomarkers to identify biosources in fresh biofilms was validated down to the genus level for Roseiflexus, Chloroflexus, and Fischerella. We identified lipid biomarkers and DNA of several new cyanobacterial species in El Tatio and reported the first detection of Fischerella biomarkers at a temperature as high as 72°C. This, together with ecological peculiarities and the proportion of clades being characterized as unclassified, illustrates the ecological singularity of El Tatio and strengthens its astrobiological relevance. The Cacao hydrothermal ecosystem was defined by a succession of microbial communities and metabolic traits associated with a high- (72°C) to low-(29°C) temperature gradient that resembled the inferred metabolic sequence events from the 16S rRNA gene universal phylogenetic tree from thermophilic to anoxygenic photosynthetic species and oxygenic phototrophs. The locally calibrated DNA-validated lipidic profile in the Cacao biofilms provided a modern (molecular and isotopic) end member to facilitate the recognition of past biosources and metabolisms from altered biomarkers records in ancient silica deposits at El Tatio analogous to Martian opaline silica structures.

Proteomic Time-Course Analysis of the Filamentous Anoxygenic Phototrophic Bacterium, Chloroflexus aurantiacus, during the Transition from Respiration to Phototrophy

Chloroflexus aurantiacus is a filamentous anoxygenic phototrophic bacterium that grows chemotrophically under oxic conditions and phototrophically under anoxic conditions. Because photosynthesis-related genes are scattered without any gene clusters in the genome, it is still unclear how this bacterium regulates protein expression in response to environmental changes. In this study, we performed a proteomic time-course analysis of how C. aurantiacus expresses proteins to acclimate to environmental changes, namely the transition from chemoheterotrophic respiratory to photoheterotrophic growth mode. Proteomic analysis detected a total of 2520 proteins out of 3934 coding sequences in the C. aurantiacus genome from samples collected at 13 time points. Almost all proteins for reaction centers, light-harvesting chlorosomes, and carbon fixation pathways were successfully detected during the growing phases in which optical densities and relative bacteriochlorophyll c contents increased simultaneously. Combination of proteomics and pigment analysis suggests that the self-aggregation of bacteriochlorophyllide c could precede the esterification of the hydrophobic farnesyl tail in cells. Cytoplasmic subunits of alternative complex III were interchanged between oxic and anoxic conditions, although membrane-bound subunits were used for both conditions. These data highlight the protein expression dynamics of phototrophy-related genes during the transition from respiration to phototrophy.

AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters

AcetoBase is a public repository and database of formyltetrahydrofolate synthetase (FTHFS) sequences. It is the first systematic collection of bacterial FTHFS nucleotide and protein sequences from genomes and metagenome-assembled genomes and of sequences generated by clone library sequencing. At its publication in 2019, AcetoBase (Version 1) was also the first database to establish connections between the FTHFS gene, the Wood–Ljungdahl pathway and 16S ribosomal RNA genes. Since the publication of AcetoBase, there have been significant improvements in the taxonomy of many bacterial lineages and accessibility/availability of public genomics and metagenomics data. The update to the AcetoBase reference database described here (Version 2) provides new sequence data and taxonomy, along with improvements in web functionality and user interface. The evaluation of this latest update by re-analysis of publicly accessible FTHFS amplicon sequencing data previously analysed with AcetoBase Version 1 revealed significant improvements in the taxonomic assignment of FTHFS sequences.

Database URL: https://acetobase.molbio.slu.se

Diversity and distribution of CO2-fixing microbial community along elevation gradients in meadow soils on the Tibetan Plateau

Soil CO₂-fixing microbes play a significant role in CO₂-fixation in the terrestrial ecosystems, particularly in the Tibetan Plateau. To understand carbon sequestration by soil CO₂-fixing microbes and the carbon cycling in alpine meadow soils, microbial diversity and their driving environmental factors were explored along an elevation gradient from 3900 to 5100 m, on both east and west slopes of Mila Mountain region on the Tibetan Plateau. The CO₂-fixing microbial communities were characterized by high-throughput sequencing targeting the cbbL gene, encoding the large subunit for the CO₂-fixing protein ribulose 1, 5-bisphosphate carboxylase/oxygenase. The overall OTU (Operational Taxonomic Unit) abundance is concentrated at an altitude between 4300  and  4900 m. The diversity of CO₂-fixing microbes is the highest in the middle altitude area, and on the east slope is higher than those on the west slope. In terms of microbial community composition, Proteobacteria is dominant, and the most abundant genera are Cupriavidus, Rhodobacter, Sulfurifustis and Thiobacillus. Altitude has the greatest influence on the structural characteristics of CO₂-fixing microbes, and other environmental factors are significantly correlated with altitude. Therefore, altitude influences the structural characteristics of CO₂-fixing microbes by driving environmental factors. Our results are helpful to understand the variation in soil microbial community and its role in soil carbon cycling along elevation gradients.

Metagenomic analysis further extends the role of Chloroflexi in fundamental biogeochemical cycles

Chloroflexi members are ubiquitous and have been extensively studied; however, the evolution and metabolic pathways of Chloroflexi members have long been debated. In the present study, the evolution and the metabolic potentials of 17 newly obtained Chloroflexi metagenome-assembled genomes (MAGs) were evaluated using genome and horizontal gene transfer (HGT) analysis. Taxonomic analysis suggests that the MAGs of the present study might be novel. One MAG encodes genes for anoxygenic phototrophy. The HGT analysis suggest that genes responsible for anoxygenic phototrophy in the MAG might have been transferred from Proteobacteria/Chlorobi. The evolution of anaerobic photosynthesis, which has long been questioned, has now been shown to be the result of HGT events. An incomplete Wood-Ljungdahl pathway (with missing genes metF, acsE, fdh, and acsA) was reported in Dehalococcoidetes members. In the present study, MAGs that were not the Dehalococcoidetes members encode genes acsA, acsB, metF and acsE. The genes responsible for sulfate reduction (sat, cysC and sir), dissimilatory sulfite reductase (dsrA and dsrB), and aerobic and anaerobic carbon monoxide oxidation (coxSML and cooSF) were detected in the present study MAGs. The present study expands our knowledge of the possible metabolic potentials of the phylum Chloroflexi and clarifies the evolution of anaerobic photosynthesis.

Phenotypic Differentiation of Autotrophic and Heterotrophic Bacterial Cells Using Raman-D2O Labeling

Carbon cycling is one of the major biogeochemical processes driven by bacteria. Autotrophic bacteria convert carbon dioxide (CO₂) into organic compounds that are used by heterotrophs. Mixotrophic bacteria can employ both autotrophy and heterotrophy for growth. The characterization of the lifestyle of individual cells is essential to understand the microbial activity and thus reveal the implication of bacteria in the carbon flux. In this study, we used groundwater bacteria to investigate the potential of Raman-D₂O labeling in combination with chemometrics to identify the carbon assimilation strategies of bacteria. Classification models were built using principal component analysis (PCA) followed by linear discriminant analysis (LDA). Autotrophs assimilated a significantly higher amount (mean C-D ratio between 16.63 and 21.69%) of deuterium than heterotrophs. The C-D signal only provides information about the activity since it appears in the Raman-silent region, where no interference with the taxonomic information is expected. The classification between autotrophs and heterotrophs achieved an overall accuracy of 96.3%. In the validation step with an independent dataset containing species not included in the model, the PCA-LDA model achieved 100% accuracy. This demonstrated that the C-D signal contributed to the identification of autotrophic and heterotrophic bacterial cells. This work reports a robust, rapid, and nondestructive approach for the identification of single cells based on their carbon acquisition strategies. The present study foresees the potential of Raman-D₂O labeling as a promising method for automated discrimination of in situ functional activities of bacteria in environmental systems.

Reconstructing the Last Common Ancestor: Epistemological and Empirical Challenges

Reconstructing the genetic traits of the Last Common Ancestor (LCA) and the Tree of Life (TOL) are two examples of the reaches of contemporary molecular phylogenetics. Nevertheless, the whole enterprise has led to paradoxical results. The presence of Lateral Gene Transfer poses epistemic and empirical challenges to meet these goals; the discussion around this subject has been enriched by arguments from philosophers and historians of science. At the same time, a few but influential research groups have aimed to reconstruct the LCA with rich-in-detail hypotheses and high-resolution gene catalogs and metabolic traits. We argue that LGT poses insurmountable challenges for detailed and rich in details reconstructions and propose, instead, a middle-ground position with the reconstruction of a slim LCA based on traits under strong pressures of Negative Natural Selection, and for the need of consilience with evidence from organismal biology and geochemistry. We defend a cautionary perspective that goes beyond the statistical analysis of gene similarities and assumes the broader consequences of evolving empirical data and epistemic pluralism in the reconstruction of early life.

Ecological variability based on lipid biomarkers in astrobiologically interesting wetlands from the Argentinian central Andes

Andean wetlands hold extremophilic communities adapted to live in harsh conditions. Here, we investigated the microbial ecology of three high-altitude hypersaline ponds from La Puna region (Argentina) showing an increasing extent of desiccation by analyzing their lipid sedimentary record. We recreated the microbial community structure and the carbon metabolisms in each lacustrine system based on the molecular distribution of lipid biomarkers and their compound-specific carbon and hydrogen isotopic signatures. We detected lipid compounds considered to be biomarkers of cyanobacteria, sulfate-reducing bacteria, purple sulfur bacteria, and archaea in the three Andean ponds, as well as diatoms in the intermediate salinity system. The relative abundance of purple sulfur and sulfate-reducing bacteria decreased with salinity, whereas cyanobacteria and archaea decreased their relative abundance in the mid-saline pond to increase it again and became both prevailing at the highest salinity. Carbon fixation in the three ponds was driven by a combination of the reductive tricarboxylic acid cycle, the reductive pentose phosphate cycle, and the reductive acetyl-CoA pathway. This work is the first to describe molecular and isotopic lipid fingerprints in wetlands from the central Andean Puna, and serves as a basis for further biogeochemical studies in the area.

Microbial Activities and Selection from Surface Ocean to Subseafloor on the Namibian Continental Shelf

Oxygen minimum zones (OMZs) are hot spots for redox-sensitive nitrogen transformations fueled by sinking organic matter. In comparison, the regulating role of sulfur-cycling microbes in marine OMZs, their impact on carbon cycling in pelagic and benthic habitats, and activities below the seafloor remain poorly understood. Using ¹³C DNA stable isotope probing (SIP) and metatranscriptomics, we explored microbial guilds involved in sulfur and carbon cycling from the ocean surface to the subseafloor on the Namibian shelf. There was a clear separation in microbial community structure across the seawater-seafloor boundary, which coincided with a 100-fold-increased concentration of microbial biomass and unique gene expression profiles of the benthic communities. ¹³C-labeled 16S rRNA genes in SIP experiments revealed carbon-assimilating taxa and their distribution across the sediment-water interface. Most of the transcriptionally active taxa among water column communities that assimilated ¹³C from diatom exopolysaccharides (mostly Bacteroidetes, Actinobacteria, Alphaproteobacteria, and Planctomycetes) also assimilated ¹³C-bicarbonate under anoxic conditions in sediment incubations. Moreover, many transcriptionally active taxa from the seafloor community (mostly sulfate-reducing Deltaproteobacteria and sulfide-oxidizing Gammaproteobacteria) that assimilated ¹³C-bicarbonate under sediment anoxic conditions also assimilated ¹³C from diatom exopolysaccharides in the surface ocean and OMZ waters. Despite strong selection at the sediment-water interface, many taxa related to either planktonic or benthic communities were found to be present at low abundance and actively assimilating carbon under both sediment and water column conditions. In austral winter, mixing of shelf waters reduces stratification and suspends sediments from the seafloor into the water column, potentially spreading metabolically versatile microbes across niches.

IMPORTANCE Microbial activities in oxygen minimum zones (OMZs) transform inorganic fixed nitrogen into greenhouse gases, impacting the Earth’s climate and nutrient equilibrium. Coastal OMZs are predicted to expand with global change and increase carbon sedimentation to the seafloor. However, the role of sulfur-cycling microbes in assimilating carbon in marine OMZs and related seabed habitats remain poorly understood. Using ¹³C DNA stable isotope probing and metatranscriptomics, we explore microbial guilds involved in sulfur and carbon cycling from ocean surface to subseafloor on the Namibian shelf. Despite strong selection and differential activities across the sediment-water interface, many active taxa were identified in both planktonic and benthic communities, either fixing inorganic carbon or assimilating organic carbon from algal biomass. Our data show that many planktonic and benthic microbes linked to the sulfur cycle can cross redox boundaries when mixing of the shelf waters reduces stratification and suspends seafloor sediment particles into the water column.

Bacterial, archaeal, and fungal community structure and interrelationships of deep-sea shrimp intestine and the surrounding sediment

Invertebrate shrimp are one of the dominant benthic macrofaunae in the deep-sea environment. The microbiota of shrimp intestine can contribute to the adaptation of their host. The impact of surrounding sediment on intestinal microbiota has been observed in cultured shrimp species, but needs to be further investigated in deep-sea shrimp. The characterization of bacterial, archaeal, and fungal community structure and their interrelationships is also limited. In this study, wild-type deep-sea shrimp and the surrounding sediment were sampled. Shrimp individuals incubated in a sediment-absent environment were also used in this study. Microbial community structure of the shrimp intestine and sediment was investigated through amplicon sequencing targeting bacterial 16S rRNA genes, archaeal 16S rRNA genes, and fungal ITS genes. The results demonstrate distinct differences in community structure between shrimp intestine and the surrounding sediment and between surface and deep (5 mbsf) sediment. The composition of the intestinal microbiota in shrimp living without sediment was different from that of wild-type shrimp, indicating that the presence or absence of sediment could influence the shrimp intestinal microbiota. Carbohydrate metabolism, energy metabolism (carbon fixation, methane metabolism, nitrogen metabolism, and sulfur metabolism), amino acid metabolism, and xenobiotic biodegradation were the most commonly predicted microbial functionalities and they interacted closely with one another. Overall, this study provided comprehensive insights into bacterial, archaeal, and fungal community structure of deep-sea shrimp intestine as well as potential ecological interactions with the surrounding sediment. This study could update our understanding of the microbiota characteristics in shrimp and sediment in deep-sea ecosystems.

Metagenome-Assembled Genomes From Pyropia haitanensis Microbiome Provide Insights Into the Potential Metabolic Functions to the Seaweed

Pyropia is an economically important edible red alga worldwide. The aquaculture industry and Pyropia production have grown considerably in recent decades. Microbial communities inhabit the algal surface and produce a variety of compounds that can influence host adaptation. Previous studies on the Pyropia microbiome were focused on the microbial components or the function of specific microbial lineages, which frequently exclude metabolic information and contained only a small fraction of the overall community. Here, we performed a genome-centric analysis to study the metabolic potential of the Pyropia haitanensis phycosphere bacteria. We reconstructed 202 unique metagenome-assembled genomes (MAGs) comprising all major taxa present within the P. haitanensis microbiome. The addition of MAGs to the genome tree containing all publicly available Pyropia-associated microorganisms increased the phylogenetic diversity by 50% within the bacteria. Metabolic reconstruction of the MAGs showed functional redundancy across taxa for pathways including nitrate reduction, taurine metabolism, organophosphorus, and 1-aminocyclopropane-1-carboxylate degradation, auxin, and vitamin B12 synthesis. Some microbial functions, such as auxin and vitamin B12 synthesis, that were previously assigned to a few Pyropia-associated microorganisms were distributed across the diverse epiphytic taxa. Other metabolic pathways, such as ammonia oxidation, denitrification, and sulfide oxidation, were confined to specific keystone taxa.

Insights into carbon-fixation pathways through metagonomics in the sediments of deep-sea cold seeps

Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean's interior. At present, six pathways of autotrophic carbon fixation have been found: the Calvin cycle, the reductive Acetyl-CoA or Wood-Ljungdahl pathway (rAcCoA), the reductive tricarboxylic acid cycle (rTCA), the 3-hydroxypropionate bicycle (3HP), the 3-hydroxypropionate/4-hydroxybutyrate cycle (3HP/4HB), and the dicarboxylate/4-hydroxybutyrate cycle (DC/4HB). Although our knowledge about carbon fixation pathways in the ocean has increased significantly, carbon fixation pathways in the cold seeps are still unknown. In this study, we collected sediment samples from two cold seeps and one trough in the south China sea (SCS), and investigated with metagenomic and metagenome assembled genomes (MAGs). We found that six autotrophic carbon fixation pathways present in the cold seeps and trough with rTCA cycle was the most common pathway, whose genes were particularly high in the cold seeps and increased with sediment depths; the rAcCoA cycle mainly occurred in the cold seep regions, and the abundance of module genes increased with sediment depths. We also elucidated members of chemoautotrophic microorganisms involved in these six carbon-fixation pathways. The rAcCoA, rTCA and DC/4-HB cycles required significantly less energy probably play an important role in the deep-sea environments, especially in the cold seeps. This study provided metabolic insights into the carbon fixation pathways in the cold seeps, and laid the foundation for future detailed study on processes and rates of carbon fixation in the deep-sea ecosystems.

Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana Trench

Viruses are ubiquitous in the oceans. Even in the deep sediments of the Mariana Trench, viruses have high productivity. However, little is known about their species composition and survival strategies in that environment. Here, we uncovered novel viral communities (3,206 viral scaffolds) in the upper slope sediments of the Mariana Trench via metagenomic analysis of 15 sediment samples. Most (99%) of the viral scaffolds lack known viral homologs, and ca. 59% of the high-quality viral genomes (total of 111 with completeness of >90%) represent novel genera, including some Phycodnaviridae and jumbo phages. These viruses contain various auxiliary metabolic genes (AMGs) potentially involved in organic carbon degradation, inorganic carbon fixation, denitrification, and assimilatory sulfate reduction, etc. This study provides novel insight into the almost unknown benthic viral communities in the Mariana Trench. IMPORTANCE The Mariana Trench harbors a substantial number of infective viral particles. However, very little is known about the identity, survival strategy, and potential functions of viruses in the trench sediments. Here, through metagenomic analysis, unusual benthic viral communities with high diversity and novelty were discovered. Among them, 59% of the viruses with a genome completeness of >90% represent novel genera. Various auxiliary metabolic genes carried by these viruses reflect the potential adaptive characteristics of viruses in this extreme environment and the biogeochemical cycles that they may participate in. This study gives us a deeper understanding of the peculiarities of viral communities in deep-sea/hadal sediments.

Ecological and Biotechnological Relevance of Mediterranean Hydrothermal Vent Systems

Marine hydrothermal systems are a special kind of extreme environments associated with submarine volcanic activity and characterized by harsh chemo-physical conditions, in terms of hot temperature, high concentrations of CO2 and H2S, and low pH. Such conditions strongly impact the living organisms, which have to develop adaptation strategies to survive. Hydrothermal systems have attracted the interest of researchers due to their enormous ecological and biotechnological relevance. From ecological perspective, these acidified habitats are useful natural laboratories to predict the effects of global environmental changes, such as ocean acidification at ecosystem level, through the observation of the marine organism responses to environmental extremes. In addition, hydrothermal vents are known as optimal sources for isolation of thermophilic and hyperthermophilic microbes, with biotechnological potential. This double aspect is the focus of this review, which aims at providing a picture of the ecological features of the main Mediterranean hydrothermal vents. The physiological responses, abundance, and distribution of biotic components are elucidated, by focusing on the necto-benthic fauna and prokaryotic communities recognized to possess pivotal role in the marine ecosystem dynamics and as indicator species. The scientific interest in hydrothermal vents will be also reviewed by pointing out their relevance as source of bioactive molecules.

Genome-resolved evidence for functionally redundant communities and novel nitrogen fixers in the deyin-1 hydrothermal field, Mid-Atlantic Ridge

BACKGROUND

Deep-sea hydrothermal vents represent unique ecosystems that redefine our understanding of the limits of life. They are widely distributed in deep oceans and typically form along mid-ocean ridges. To date, the hydrothermal systems in the Mid-Atlantic Ridge south of 14°S remain barely explored, limiting our understanding of the microbial community in this distinct ecosystem. The Deyin-1 is a newly discovered hydrothermal field in this area. By applying the metagenomic analysis, we aim at gaining much knowledge of the biodiversity and functional capability of microbial community inhabiting this field.

RESULTS

In the current study, 219 metagenomic assembled genomes (MAGs) were reconstructed, unveiling a diverse and variable community dominated by Bacteroidetes, Nitrospirae, Alpha-, Delta-, and Gammaproteobacteria in the active and inactive chimney samples as well as hydrothermal oxide samples. Most of these major taxa were potentially capable of using reduced sulfur and hydrogen as primary energy sources. Many members within the major taxa exhibited potentials of metabolic plasticity by possessing multiple energy metabolic pathways. Among these samples, different bacteria were found to be the major players of the same metabolic pathways, further supporting the variable and functionally redundant community in situ. In addition, a high proportion of MAGs harbored the genes of carbon fixation and extracellular carbohydrate-active enzymes, suggesting that both heterotrophic and autotrophic strategies could be essential for their survival. Notably, for the first time, the genus Candidatus Magnetobacterium was shown to potentially fix nitrogen, indicating its important role in the nitrogen cycle of inactive chimneys. Moreover, the metabolic plasticity of microbes, diverse and variable community composition, and functional redundancy of microbial communities may represent the adaptation strategies to the geochemically complex and fluctuating environmental conditions in deep-sea hydrothermal fields.

CONCLUSIONS

This represents the first assembled-genome-based investigation into the microbial community and metabolism of a hydrothermal field in the Mid-Atlantic Ridge south of 14°S. The findings revealed that a high proportion of microbes could benefit from simultaneous use of heterotrophic and autotrophic strategies in situ. It also presented novel members of potential diazotrophs and highlighted the metabolic plasticity and functional redundancy across deep-sea hydrothermal systems. Video abstract.

Biota-mediated carbon cycling-A synthesis of biotic-interaction controls on blue carbon

Research into biotic interactions has been a core theme of ecology for over a century. However, despite the obvious role that biota play in the global carbon cycle, the effects of biotic interactions on carbon pools and fluxes are poorly understood. Here we develop a conceptual framework that illustrates the importance of biotic interactions in regulating carbon cycling based on a literature review and a quantitative synthesis by means of meta-analysis. Our study focuses on blue carbon ecosystems-vegetated coastal ecosystems that function as the most effective long-term CO₂ sinks of the biosphere. We demonstrate that a multitude of mutualistic, competitive and consumer-resource interactions between plants, animals and microbiota exert strong effects on carbon cycling across various spatial scales ranging from the rhizosphere to the landscape scale. Climate change-sensitive abiotic factors modulate the strength of biotic-interaction effects on carbon fluxes, suggesting that the importance of biota-mediated carbon cycling will change under future climatic conditions. Strong effects of biotic interactions on carbon cycling imply that biosphere-climate feedbacks may not be sufficiently represented in current Earth system models. Inclusion of new functional groups in these models, and new approaches to simplify species interactions, may thus improve the predictions of biotic effects on the global climate.

Transcriptomic evidences for microbial carbon and nitrogen cycles in the deoxygenated seawaters of Bohai Sea

Eutrophication-induced water deoxygenation occurs continually in coastal oceans, and alters community structure, metabolic processes, and the energy shunt, resulting in a major threat to the ecological environment. Seasonal deoxygenation events have occurred in the Bohai Sea (China), however, how these affect the functional activity of microorganisms remains unclear. Here, through the use of absolute quantification of 16S rRNA genes amplicon sequencing and metatranscriptomics approaches, we investigated the structure of the microbial community and the patterns of transcriptional activity in deoxygenated seawaters. The dominant phyla were Proteobacteria (average value, 1.4 × 10⁶ copies ml^-1), Cyanobacteria (3.7 × 10⁵ copies ml^-1), Bacteroidetes (2.7 × 10⁵ copies ml^-1), and the ammonia-oxidizing archaea Thaumarchaeota (1.9 × 10⁵ copies ml^-1). Among the various environmental factors, dissolved oxygen, pH and temperature displayed the most significant correlation with microbial community composition and functional activity. Metatranscriptomic data showed high transcriptional activity of Thaumarchaeota in the deoxygenated waters, with a significant increase in the expression of core genes representing ammonia oxidation, ammonia transport, and carbon fixation (3-hydroxypropionic acid/4-hydroxybutyric acid cycle) pathways. The transcripts of Cyanobacteria involved in photosynthesis and carbon fixation (Calvin-Benson-Bassham cycle) significantly decreased in low oxygen waters. Meanwhile, the transcripts for the ribulose bisphosphate carboxylase-encoding gene shifted from being assigned to photoautotrophic to chemoautotrophic organisms in surface and bottom waters, respectively. Moreover, the transcription profile indicated that heterotrophs play a critical role in transforming low-molecular-weight dissolved organic nitrogen. Elevated abundances of transcripts related to microbial antioxidant activity corresponded to an enhanced aerobic metabolism of Thaumarchaeota in the low oxygen seawater. In general, our transcriptional evidences showed a population increase of Thaumarchaeota, especially the coastal ecotype of ammonia oxidizers, in low oxygen aquatic environments, and indicated an enhanced contribution of chemolithoautotrophic carbon fixation to carbon flow.

Genetic Potential of Dissulfurimicrobium hydrothermale, an Obligate Sulfur-Disproportionating Thermophilic Microorganism

The biochemical pathways of anaerobic sulfur disproportionation are only partially deciphered, and the mechanisms involved in the first step of S⁰-disproportionation remain unknown. Here, we present the results of sequencing and analysis of the complete genome of Dissulfurimicrobium hydrothermale strain Sh68^T, one of two strains isolated to date known to grow exclusively by anaerobic disproportionation of inorganic sulfur compounds. Dissulfurimicrobium hydrothermale Sh68^T is a motile, thermophilic, anaerobic, chemolithoautotrophic microorganism isolated from a hydrothermal pond at Uzon caldera, Kamchatka, Russia. It is able to produce energy and grow by disproportionation of elemental sulfur, sulfite and thiosulfate. Its genome consists of a circular chromosome of 2,025,450 base pairs, has a G + C content of 49.66% and a completion of 97.6%. Genomic data suggest that CO₂ assimilation is carried out by the Wood–Ljungdhal pathway and that central anabolism involves the gluconeogenesis pathway. The genome of strain Sh68^T encodes the complete gene set of the dissimilatory sulfate reduction pathway, some of which are likely to be involved in sulfur disproportionation. A short sequence protein of unknown function present in the genome of strain Sh68^T is conserved in the genomes of a large panel of other S⁰-disproportionating bacteria and was absent from the genomes of microorganisms incapable of elemental sulfur disproportionation. We propose that this protein may be involved in the first step of elemental sulfur disproportionation, as S⁰ is poorly soluble and unable to cross the cytoplasmic membrane in this form.

The Deep Rocky Biosphere: New Geomicrobiological Insights and Prospects

Rocks that react with liquid water are widespread but spatiotemporally limited throughout the solar system, except for Earth. Rock-forming minerals with high iron content and accessory minerals with high amounts of radioactive elements are essential to support rock-hosted microbial life by supplying organics, molecular hydrogen, and/or oxidants. Recent technological advances have broadened our understanding of the rocky biosphere, where microbial inhabitation appears to be difficult without nutrient and energy inputs from minerals. In particular, microbial proliferation in igneous rock basements has been revealed using innovative geomicrobiological techniques. These recent findings have dramatically changed our perspective on the nature and the extent of microbial life in the rocky biosphere, microbial interactions with minerals, and the influence of external factors on habitability. This study aimed to gather information from scientific and/or technological innovations, such as omics-based and single-cell level characterizations, targeting deep rocky habitats of organisms with minimal dependence on photosynthesis. By synthesizing pieces of rock-hosted life, we can explore the evo-phylogeny and ecophysiology of microbial life on Earth and the life’s potential on other planetary bodies.

Energy at Origins: Favorable Thermodynamics of Biosynthetic Reactions in the Last Universal Common Ancestor (LUCA)

Though all theories for the origin of life require a source of energy to promote primordial chemical reactions, the nature of energy that drove the emergence of metabolism at origins is still debated. We reasoned that evidence for the nature of energy at origins should be preserved in the biochemical reactions of life itself, whereby changes in free energy, ΔG, which determine whether a reaction can go forward or not, should help specify the source. By calculating values of ΔG across the conserved and universal core of 402 individual reactions that synthesize amino acids, nucleotides and cofactors from H2, CO2, NH3, H2S and phosphate in modern cells, we find that 95-97% of these reactions are exergonic (ΔG ≤ 0 kJ⋅mol-1) at pH 7-10 and 80-100°C under nonequilibrium conditions with H2 replacing biochemical reductants. While 23% of the core's reactions involve ATP hydrolysis, 77% are ATP-independent, thermodynamically driven by ΔG of reactions involving carbon bonds. We identified 174 reactions that are exergonic by -20 to -300 kJ⋅mol-1 at pH 9 and 80°C and that fall into ten reaction types: six pterin dependent alkyl or acyl transfers, ten S-adenosylmethionine dependent alkyl transfers, four acyl phosphate hydrolyses, 14 thioester hydrolyses, 30 decarboxylations, 35 ring closure reactions, 31 aromatic ring formations, and 44 carbon reductions by reduced nicotinamide, flavins, ferredoxin, or formate. The 402 reactions of the biosynthetic core trace to the last universal common ancestor (LUCA), and reveal that synthesis of LUCA's chemical constituents required no external energy inputs such as electric discharge, UV-light or phosphide minerals. The biosynthetic reactions of LUCA uncover a natural thermodynamic tendency of metabolism to unfold from energy released by reactions of H2, CO2, NH3, H2S, and phosphate.

Microbial diversity and function in crystalline basement beneath the Deccan Traps explored in a 3 km borehole at Koyna, western India

Deep terrestrial subsurface represents a huge repository of global prokaryotic biomass. Given its vastness and importance, microbial life within the deep subsurface continental crust remains under-represented in global studies. We characterize the microbial communities of deep, extreme and oligotrophic realm hosted by crystalline Archaean granitic rocks underneath the Deccan Traps, through sampling via 3000 m deep scientific borehole at Koyna, India through metagenomics, amplicon sequencing and cultivation-based analyses. Gene sequences 16S rRNA (7.37 × 10⁶ ) show considerable bacterial diversity and the existence of a core microbiome (5724 operational taxonomic units conserved out of a total 118,064 OTUs) across the depths. Relative abundance of different taxa of core microbiome varies with depth in response to prevailing lithology and geochemistry. Co-occurrence network analysis and cultivation attempt to elucidate close interactions among autotrophic and organotrophic bacteria. Shotgun metagenomics reveals a major role of autotrophic carbon fixation via the Wood-Ljungdahl pathway and genes responsible for energy and carbon metabolism. Deeper analysis suggests the existence of an 'acetate switch', coordinating biosynthesis and cellular homeostasis. We conclude that the microbial life in the nutrient- and energy-limited deep granitic crust is constrained by the depth and managed by a few core members via a close interplay between autotrophy and organotrophy.

Lineage-specific energy and carbon metabolism of sponge symbionts and contributions to the host carbon pool

Marine sponges host a wide diversity of microorganisms, which have versatile modes of carbon and energy metabolism. In this study we describe the major lithoheterotrophic and autotrophic processes in 21 microbial sponge-associated phyla using novel and existing genomic and transcriptomic datasets. We show that the main microbial carbon fixation pathways in sponges are the Calvin–Benson–Bassham cycle (energized by light in Cyanobacteria, by sulfur compounds in two orders of Gammaproteobacteria, and by a wide range of compounds in filamentous Tectomicrobia), the reductive tricarboxylic acid cycle (used by Nitrospirota), and the 3-hydroxypropionate/4-hydroxybutyrate cycle (active in Thaumarchaeota). Further, we observed that some sponge symbionts, in particular Acidobacteria, are capable of assimilating carbon through anaplerotic processes. The lithoheterotrophic lifestyle was widespread and CO oxidation is the main energy source for sponge lithoheterotrophs. We also suggest that the molybdenum-binding subunit of dehydrogenase (encoded by coxL) likely evolved to benefit also organoheterotrophs that utilize various organic substrates. Genomic potential does not necessarily inform on actual contribution of autotrophs to light and dark carbon budgets. Radioisotope assays highlight variability in the relative contributions of photo- and chemoautotrophs to the total carbon pool across different sponge species, emphasizing the importance of validating genomic potential with physiology experimentation.

Comparative Metagenomic Analysis of Two Hot Springs From Ourense (Northwestern Spain) and Others Worldwide

With their circumneutral pH and their moderate temperature (66 and 68°C, respectively), As Burgas and Muiño da Veiga are two important human-use hot springs, previously studied with traditional culture methods, but never explored with a metagenomic approach. In the present study, we have performed metagenomic sequence-based analyses to compare the taxonomic composition and functional potential of these hot springs. Proteobacteria, Deinococcus-Thermus, Firmicutes, Nitrospirae, and Aquificae are the dominant phyla in both geothermal springs, but there is a significant difference in the abundance of these phyla between As Burgas and Muiño da Veiga. Phylum Proteobacteria dominates As Burgas ecosystem while Aquificae is the most abundant phylum in Muiño da Veiga. Taxonomic and functional analyses reveal that the variability in water geochemistry might be shaping the differences in the microbial communities inhabiting these geothermal springs. The content in organic compounds of As Burgas water promotes the presence of heterotrophic populations of the genera Acidovorax and Thermus, whereas the sulfate-rich water of Muiño da Veiga favors the co-dominance of genera Sulfurihydrogenibium and Thermodesulfovibrio. Differences in ammonia concentration exert a selective pressure toward the growth of nitrogen-fixing bacteria such as Thermodesulfovibrio in Muiño da Veiga. Temperature and pH are two important factors shaping hot springs microbial communities as was determined by comparative analysis with other thermal springs.

Ecological Dichotomies Arise in Microbial Communities Due to Mixing of Deep Hydrothermal Waters and Atmospheric Gas in a Circumneutral Hot Spring

Little is known of how the confluence of subsurface and surface processes influences the assembly and habitability of hydrothermal ecosystems. To address this knowledge gap, the geochemical and microbial composition of a high-temperature, circumneutral hot spring in Yellowstone National Park was examined to identify the sources of solutes and their effect on the ecology of microbial inhabitants. Metagenomic analysis showed that populations comprising planktonic and sediment communities are archaeal dominated, are dependent on chemical energy (chemosynthetic), share little overlap in their taxonomic composition, and are differentiated by their inferred use of/tolerance to oxygen and mode of carbon metabolism. The planktonic community is dominated by putative aerobic/aerotolerant autotrophs, while the taxonomic composition of the sediment community is more evenly distributed and comprised of anaerobic heterotrophs. These observations are interpreted to reflect sourcing of the spring by anoxic, organic carbon-limited subsurface hydrothermal fluids and ingassing of atmospheric oxygen that selects for aerobic/aerotolerant organisms that have autotrophic capabilities in the water column. Autotrophy and consumption of oxygen by the planktonic community may influence the assembly of the anaerobic and heterotrophic sediment community. Support for this inference comes from higher estimated rates of genome replication in planktonic populations than sediment populations, indicating faster growth in planktonic populations. Collectively, these observations provide new insight into how mixing of subsurface waters and atmospheric oxygen create dichotomy in the ecology of hot spring communities and suggest that planktonic and sediment communities may have been less differentiated taxonomically and functionally prior to the rise of oxygen at ∼2.4 billion years ago (Gya). IMPORTANCE Understanding the source and availability of energy capable of supporting life in hydrothermal environments is central to predicting the ecology of microbial life on early Earth when volcanic activity was more widespread. Little is known of the substrates supporting microbial life in circumneutral to alkaline springs, despite their relevance to early Earth habitats. Using metagenomic and informatics approaches, water column and sediment habitats in a representative circumneutral hot spring in Yellowstone were shown to be dichotomous, with the former largely hosting aerobic/aerotolerant autotrophs and the latter primarily hosting anaerobic heterotrophs. This dichotomy is attributed to influx of atmospheric oxygen into anoxic deep hydrothermal spring waters. These results indicate that the ecology of microorganisms in circumneutral alkaline springs sourced by deep hydrothermal fluids was different prior to the rise of atmospheric oxygen ∼2.4 Gya, with planktonic and sediment communities likely to be less differentiated than contemporary circumneutral hot springs.

Post-translational Lysine Ac(et)ylation in Bacteria: A Biochemical, Structural, and Synthetic Biological Perspective

Ac(et)ylation is a post-translational modification present in all domains of life. First identified in mammals in histones to regulate RNA synthesis, today it is known that is regulates fundamental cellular processes also in bacteria: transcription, translation, metabolism, cell motility. Ac(et)ylation can occur at the ε-amino group of lysine side chains or at the α-amino group of a protein. Furthermore small molecules such as polyamines and antibiotics can be acetylated and deacetylated enzymatically at amino groups. While much research focused on N-(ε)-ac(et)ylation of lysine side chains, much less is known about the occurrence, the regulation and the physiological roles on N-(α)-ac(et)ylation of protein amino termini in bacteria. Lysine ac(et)ylation was shown to affect protein function by various mechanisms ranging from quenching of the positive charge, increasing the lysine side chains’ size affecting the protein surface complementarity, increasing the hydrophobicity and by interfering with other post-translational modifications. While N-(ε)-lysine ac(et)ylation was shown to be reversible, dynamically regulated by lysine acetyltransferases and lysine deacetylases, for N-(α)-ac(et)ylation only N-terminal acetyltransferases were identified and so far no deacetylases were discovered neither in bacteria nor in mammals. To this end, N-terminal ac(et)ylation is regarded as being irreversible. Besides enzymatic ac(et)ylation, recent data showed that ac(et)ylation of lysine side chains and of the proteins N-termini can also occur non-enzymatically by the high-energy molecules acetyl-coenzyme A and acetyl-phosphate. Acetyl-phosphate is supposed to be the key molecule that drives non-enzymatic ac(et)ylation in bacteria. Non-enzymatic ac(et)ylation can occur site-specifically with both, the protein primary sequence and the three dimensional structure affecting its efficiency. Ac(et)ylation is tightly controlled by the cellular metabolic state as acetyltransferases use ac(et)yl-CoA as donor molecule for the ac(et)ylation and sirtuin deacetylases use NAD⁺ as co-substrate for the deac(et)ylation. Moreover, the accumulation of ac(et)yl-CoA and acetyl-phosphate is dependent on the cellular metabolic state. This constitutes a feedback control mechanism as activities of many metabolic enzymes were shown to be regulated by lysine ac(et)ylation. Our knowledge on lysine ac(et)ylation significantly increased in the last decade predominantly due to the huge methodological advances that were made in fields such as mass-spectrometry, structural biology and synthetic biology. This also includes the identification of additional acylations occurring on lysine side chains with supposedly different regulatory potential. This review highlights recent advances in the research field. Our knowledge on enzymatic regulation of lysine ac(et)ylation will be summarized with a special focus on structural and mechanistic characterization of the enzymes, the mechanisms underlying non-enzymatic/chemical ac(et)ylation are explained, recent technological progress in the field are presented and selected examples highlighting the important physiological roles of lysine ac(et)ylation are summarized.

Time-Integrative Multibiomarker Detection in Triassic-Jurassic Rocks from the Atacama Desert: Relevance to the Search for Basic Life Beyond Earth

Detecting evidence of life on other planetary bodies requires a certain understanding of known biomarkers and their chemical nature, preservation potential, or biological specificity. In a planetary search for life, carbonates are of special interest due to their known association with life as we know it. On Earth, carbonates serve as an invaluable paleogeochemical archive of fossils of up to billions of years old. Here, we investigated biomarker profiles on three Chilean Triassic-Jurassic sedimentary records regarding our search for signs of past and present life over ∼200 Ma. A multianalytical platform that combines lipid-derived biomarkers, metaproteomics, and a life detector chip (LDChip) is considered in the detection of biomolecules with different perdurability and source-diagnosis potential. The combined identification of proteins with positive LDChip inmunodetections provides metabolic information and taxonomic affiliation of modern/subrecent biosignatures. Molecular and isotopic analysis of more perdurable hydrocarbon cores allows for the identification of general biosources and dominant autotrophic pathways over time, as well as recreation of prevailing redox conditions over ∼200 Ma. We demonstrate how extraterrestrial life detection can benefit from the use of different biomarkers to overcome diagnosis limitations due to a lack of specificity and/or alteration over time. Our findings have implications for future astrobiological missions to Mars.

Carbon Farming: Prospects and Challenges

Carbon farming is a capable strategy for more sustainable production of food and other related products. It seeks to produce a diverse array of natural farming methods and marketable products simultaneously. According to the food and agriculture organization (FAO), agriculture, forestry, and other land-use practices account for 24% of global greenhouse gas (GHG) emissions and total global livestock emissions of 7.1 gigatons of CO2-equivalent per year, representing 14.5% of total anthropogenic GHG emissions. For example, an agroforestry system that deliberately integrates trees and crops with livestock in agricultural production could potentially increase carbon sequestration and decrease GHG emissions from terrestrial ecosystems, thus helping to mitigate global climatic change. Also, agroforestry is capable of generating huge amounts of bio-mass and is believed to be particularly suitable for replenishing soil organic carbon (SOC). SOC is a crucial indicator for soil fertility since the change in SOC can explain whether the land use pattern degrades or improves soil fertility. Moreover, SOC found in soil in the form of soil organic matter (SOM) helps to improve soil health either directly or indirectly. Thus, efforts should be made to convince farmers to increase their resource-use efficiency and soil conserving ability to get maximum benefits from agriculture. Therefore, this review aimed at clarification about carbon farming, modifications in carbon cycle and carbon sequestration during agricultural development, and benefits of agroforestry.

Comparative Metagenomics of the Active Layer and Permafrost from Low-Carbon Soil in the Canadian High Arctic

Approximately 87% of the Arctic consists of low-organic carbon mineral soil, but knowledge of microbial activity in low-carbon permafrost (PF) and active layer soils remains limited. This study investigated the taxonomic composition and genetic potential of microbial communities at contrasting depths of the active layer (5, 35, and 65 cm below surface, bls) and PF (80 cm bls). We showed microbial communities in PF to be taxonomically and functionally different from those in the active layer. 16S rRNA gene sequence analysis revealed higher biodiversity in the active layer than in PF, and biodiversity decreased significantly with depth. The reconstructed 91 metagenome-assembled genomes showed that PF was dominated by heterotrophic, fermenting Bacteroidota using nitrite as their main electron acceptor. Prevalent microbes identified in the active layer belonged to bacterial taxa, gaining energy via aerobic respiration. Gene abundance in metagenomes revealed enrichment of genes encoding the plant-derived polysaccharide degradation and metabolism of nitrate and sulfate in PF, whereas genes encoding methane/ammonia oxidation, cold-shock protein, and two-component systems were generally more abundant in the active layer, particularly at 5 cm bls. The results of this study deepen our understanding of the low-carbon Arctic soil microbiome and improve prediction of the impacts of thawing PF.

Chemical Basis of Carbon Fixation Autotrophic Paleometabolism

Abstract

On the basis of biomimetic, phylometabolic, and thermodynamic analysis of modern CO2 assimilation pathways, a paleophenotypic reconstruction of ancient autotrophic metabolism systems was carried out. As a chemical basis for CO2 fixation paleometabolism, metabolic networks capable of self-reproduction and evolution are considered, and the reversibility of the transformation reactions of its intermediates is the most important factor in self-development of this network. The substances of the C–H–O system, paragenetically associated with hydrocarbons, create a phase space, which is a set of universal intermediates of the autotrophic paleometabolism chemical network. The concept of two strategies for the origin and development of autotrophic carbon fixation paleometabolism in the oxidized (CO2) and reduced (CH4) redox regimes of degassing of the ancient Earth is proposed. It was shown that P, T, and the redox conditions of hydrothermal systems of the early Archean were favorable for the development of primary methanotrophic metabolism.

Bog ecosystems as a playground for plant-microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria

BACKGROUND

Bogs are unique ecosystems inhabited by distinctive, coevolved assemblages of organisms, which play a global role for carbon storage, climate stability, water quality and biodiversity. To understand ecology and plant-microbe co-occurrence in bogs, we selected 12 representative species of bryophytes and vascular plants and subjected them to a shotgun metagenomic sequencing approach. We explored specific plant-microbe associations as well as functional implications of the respective communities on their host plants and the bog ecosystem.

RESULTS

Microbial communities were shown to be functionally adapted to their plant hosts; a higher colonization specificity was found for vascular plants. Bryophytes that commonly constitute the predominant Sphagnum layer in bogs were characterized by a higher bacterial richness and diversity. Each plant group showed an enrichment of distinct phylogenetic and functional bacterial lineages. Detailed analyses of the metabolic potential of 28 metagenome-assembled genomes (MAGs) supported the observed functional specification of prevalent bacteria. We found that novel lineages of Betaproteobacteria and Actinobacteria in the bog environment harboured genes required for carbon fixation via RuBisCo. Interestingly, several of the highly abundant bacteria in both plant types harboured pathogenicity potential and carried similar virulence factors as found with corresponding human pathogens.

CONCLUSIONS

The unexpectedly high specificity of the plant microbiota reflects intimate plant-microbe interactions and coevolution in bog environments. We assume that the detected pathogenicity factors might be involved in coevolution processes, but the finding also reinforces the role of the natural plant microbiota as a potential reservoir for human pathogens. Overall, the study demonstrates how plant-microbe assemblages can ensure stability, functioning and ecosystem health in bogs. It also highlights the role of bog ecosystems as a playground for plant-microbe coevolution. Video abstract.

Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses

Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between chemosynthetic bacteria and eukaryotes and that these chemosymbioses are ubiquitous in both deep-sea and shallow-water environments. The symbionts are primary producers that gain energy from the oxidation of reduced compounds, such as sulfide and methane, to fix carbon dioxide or methane into biomass to feed their hosts. This review outlines how the symbiotic partners have adapted to living together. We first focus on the phylogenetic and metabolic diversity of these symbioses and then highlight selected research directions that could advance our understanding of the processes that shaped the evolutionary and ecological success of these associations. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The curious consistency of carbon biosignatures over billions of years of Earth-life coevolution

The oldest and most wide-ranging signal of biological activity (biosignature) on our planet is the carbon isotope composition of organic materials preserved in rocks. These biosignatures preserve the long-term evolution of the microorganism-hosted metabolic machinery responsible for producing deviations in the isotopic compositions of inorganic and organic carbon. Despite billions of years of ecosystem turnover, evolutionary innovation, organismic complexification, and geological events, the organic carbon that is a residuum of the global marine biosphere in the rock record tells an essentially static story. The ~25‰ mean deviation between inorganic and organic 13C/12C values has remained remarkably unchanged over >3.5 billion years. The bulk of this record is conventionally attributed to early-evolved, RuBisCO-mediated CO2 fixation that, in extant oxygenic phototrophs, produces comparable isotopic effects and dominates modern primary production. However, billions of years of environmental transition, for example, in the progressive oxygenation of the Earth's atmosphere, would be expected to have accompanied shifts in the predominant RuBisCO forms as well as enzyme-level adaptive responses in RuBisCO CO2-specificity. These factors would also be expected to result in preserved isotopic signatures deviating from those produced by extant RuBisCO in oxygenic phototrophs. Why does the bulk carbon isotope record not reflect these expected environmental transitions and evolutionary innovations? Here, we discuss this apparent discrepancy and highlight the need for greater quantitative understanding of carbon isotope fractionation behavior in extant metabolic pathways. We propose novel, laboratory-based approaches to reconstructing ancestral states of carbon metabolisms and associated enzymes that can constrain isotopic biosignature production in ancient biological systems. Together, these strategies are crucial for integrating the complementary toolsets of biological and geological sciences and for interpretation of the oldest record of life on Earth.

"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.

Substrate usage determines carbon flux via the citrate cycle in Helicobacter pylori

Helicobacter pylori displays a worldwide infection rate of about 50%. The Gram-negative bacterium is the main reason for gastric cancer and other severe diseases. Despite considerable knowledge about the metabolic inventory of H. pylori, carbon fluxes through the citrate cycle (TCA cycle) remained enigmatic. In this study, different ¹³ C-labeled substrates were supplied as carbon sources to H. pylori during microaerophilic growth in a complex medium. After growth, ¹³ C-excess and ¹³ C-distribution were determined in multiple metabolites using GC-MS analysis. [U-¹³ C₆ ]Glucose was efficiently converted into glyceraldehyde but only less into TCA cycle-related metabolites. In contrast, [U-¹³ C₅ ]glutamate, [U-¹³ C₄ ]succinate, and [U-¹³ C₄ ]aspartate were incorporated at high levels into intermediates of the TCA cycle. The comparative analysis of the ¹³ C-distributions indicated an adaptive TCA cycle fully operating in the closed oxidative direction with rapid equilibrium fluxes between oxaloacetate-succinate and α-ketoglutarate-citrate. ¹³ C-Profiles of the four-carbon intermediates in the TCA cycle, especially of malate, together with the observation of an isocitrate lyase activity by in vitro assays, suggested carbon fluxes via a glyoxylate bypass. In conjunction with the lack of enzymes for anaplerotic CO₂ fixation, the glyoxylate bypass could be relevant to fill up the TCA cycle with carbon atoms derived from acetyl-CoA.

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

The deep sea, the largest ocean's compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.

Bacterial community in saline farmland soil on the Tibetan plateau: responding to salinization while resisting extreme environments

Background

Salinization damages the health of soil systems and reduces crop yields. Responses of microbial communities to salinized soils and their functional maintenance under high salt stress are valuable scientific problems. Meanwhile, the microbial community of the salinized soil in the plateau environment is less understood. Here, we applied metagenomics technology to reveal the structure and function of microorganisms in salinized soil of the Tibetan Plateau.

Results

The diversity of composition and function of microbial community in saline soil have changed significantly. The abundances of chemoautotrophic and acidophilic bacteria comprising Rhodanobacter, Acidobacterium, Candidatus Nitrosotalea, and Candidatus Koribacter were significantly higher in saline soil. The potential degradation of organic carbon in the saline soil, as well as the production of NO and N₂O via denitrification, and the production of sulfate by sulfur oxidation were significantly higher than the non-saline soil. Both types of soils were rich in genes encoding resistance to environmental stresses (i.e., cold, ultraviolet light, and hypoxia in Tibetan Plateau). The resistance of the soil microbial communities to the saline environment is based on the absorption of K⁺ as the main mechanism, with cross-protection proteins and absorption buffer molecules as auxiliary mechanisms in our study area. Network analysis showed that functional group comprising chemoautotrophic and acidophilic bacteria had significant positive correlations with electrical conductivity and total sulfur, and significant negative correlations with the total organic carbon, pH, and available nitrogen. The soil moisture, pH, and electrical conductivity are likely to affect the bacterial carbon, nitrogen, and sulfur cycles.

Conclusions

These results indicate that the specific environment of the Tibetan Plateau and salinization jointly shape the structure and function of the soil bacterial community, and that the bacterial communities respond to complex and harsh living conditions. In addition, environmental feedback probably exacerbates greenhouse gas emissions and accelerates the reduction in the soil pH. This study will provide insights into the microbial responses to soil salinization and the potential ecological risks in the special plateau environment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02190-6.

Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome

The unique combination of depth, salinity, and water masses make the South Atlantic Ocean an ecosystem of special relevance within the global ocean. Yet, the microbiome of this ecosystem has received less attention than other regions of the global Ocean. This has hampered our understanding of the diversity and metabolic potential of the microorganisms that dwell in this habitat. To fill this knowledge gap, we analyzed a collection of 31 metagenomes from the Atlantic Ocean that spanned the epipelagic, mesopelagic and bathypelagic zones (surface to 4000 m). Read-centric and gene-centric analysis revealed the unique taxonomic and functional composition of metagenomes from each depth zone, which was driven by differences in physical and chemical parameters. In parallel, a total of 40 metagenome-assembled genomes were obtained, which recovered one third of the total community. Phylogenomic reconstruction revealed that many of these genomes are derived from poorly characterized taxa of Bacteria and Archaea. Genomes derived from heterotrophic bacteria of the aphotic zone displayed a large apparatus of genes suited for the utilization of recalcitrant organic compounds such as cellulose, chitin and alkanes. In addition, we found genomic evidence suggesting that mixotrophic bacteria from the bathypelagic zone could perform carbon fixation through the Calvin-Benson-Bassham cycle, fueled by sulfur oxidation. Finally, we found that the viral communities shifted throughout the water column regarding their targeted hosts and virus-to-microbe ratio, in response to shifts in the composition and functioning their microbial counterparts. Our findings shed light on the microbial and viral drivers of important biogeochemical processes that take place in the South Atlantic Ocean.

Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria

BACKGROUND

Free-living and symbiotic chemosynthetic microbial communities support primary production and higher trophic levels in deep-sea hydrothermal vents. The shrimp Rimicaris exoculata, which dominates animal communities along the Mid-Atlantic Ridge, houses a complex bacterial community in its enlarged cephalothorax. The dominant bacteria present are from the taxonomic groups Campylobacteria, Desulfobulbia (formerly Deltaproteobacteria), Alphaproteobacteria, Gammaproteobacteria, and some recently discovered iron oxyhydroxide-coated Zetaproteobacteria. This epibiotic consortium uses iron, sulfide, methane, and hydrogen as energy sources. Here, we generated shotgun metagenomes from Rimicaris exoculata cephalothoracic epibiotic communities to reconstruct and investigate symbiotic genomes. We collected specimens from three geochemically contrasted vent fields, TAG, Rainbow, and Snake Pit, to unravel the specificity, variability, and adaptation of Rimicaris-microbe associations.

RESULTS

Our data enabled us to reconstruct 49 metagenome-assembled genomes (MAGs) from the TAG and Rainbow vent fields, including 16 with more than 90% completion and less than 5% contamination based on single copy core genes. These MAGs belonged to the dominant Campylobacteria, Desulfobulbia, Thiotrichaceae, and some novel candidate phyla radiation (CPR) lineages. In addition, most importantly, two MAGs in our collection were affiliated to Zetaproteobacteria and had no close relatives (average nucleotide identity ANI < 77% with the closest relative Ghiorsea bivora isolated from TAG, and 88% with each other), suggesting potential novel species. Genes for Calvin-Benson Bassham (CBB) carbon fixation, iron, and sulfur oxidation, as well as nitrate reduction, occurred in both MAGs. However, genes for hydrogen oxidation and multicopper oxidases occurred in one MAG only, suggesting shared and specific potential functions for these two novel Zetaproteobacteria symbiotic lineages. Overall, we observed highly similar symbionts co-existing in a single shrimp at both the basaltic TAG and ultramafic Rainbow vent sites. Nevertheless, further examination of the seeming functional redundancy among these epibionts revealed important differences.

CONCLUSION

These data highlight microniche partitioning in the Rimicaris holobiont and support recent studies showing that functional diversity enables multiple symbiont strains to coexist in animals colonizing hydrothermal vents. Video Abstract.