A) Genome-based (metagenome-resolved genomes) ecological and evolutionary studies
The genome-resolved methods present significant advantages over previously used approaches such as read-based and homology-based analyses that give us a low-resolution of microbial communities and no information on which genes and pathways are co-located on individual genomes. Correctly assigning genes to genomes and determining the direction of enzymatic operation of microbial metabolism needs a refined knowledge of their operon structure and organismal context. This can be achieved by the genome-resolved approaches. We have used this approach to discover novel/newly identified archaeal groups from marine environments, including Hydrothermarchaeota, Bathyarchaeota, Thermoprofundales, Woesearchaeota, and Asgard superphylum (a novel archaeal superphylum). The genomic/transcriptomic inferences have provided new insights into their ecology, evolution, metabolism, and activities.
The metagenome-resolved genome-based microbial community study allows fine-scale researches on microbial metabolism. This approach enables us to understand the evolution and ecology basis and internal and external networking of a system across a variety of spatial and temporal scales. We studied the Proteobacteria functions in marine hydrothermal settings and their genomic diversification towards wide environment adaption in the ocean (The ISME Journal 14, 2060–2077 (2020)). We have uncovered the significant metabolic role of Gammaproteobacteria members in mediating methyl-, sulfur-, and petroleum organic compound utilization in deep ocean hydrothermal plume (The ISME Journal DOI: 10.1038/s41396-020-00745-5 (2020)). We have conducted comprehensive meta-analysis on the Thermoprofundales 16S rRNA sequences, discovered segregations of Thermoprofundales subgroups toward salinity and methane seeps and the non-random association of Thermoprofundales with Lokiarchaeota in many environments, and unraveled their metabolic potentials and ecological functions based on omics techniques (The ISME Journal, doi: 10.1038/s41396-018-0321-8 (2018)). Meanwhile, we also made efforts on advancing bioinformatic tools for biogeochemical analysis. we have developed a new software tool – METABOLIC (link) – for scalable high-throughput metabolic and biogeochemical functional trait profiling based on microbial genomes (bioRxiv, doi: https://doi.org/10.1101/761643 (2019)).
METabolic And BiogeOchemistry anaLyses In miCrobes
https://github.com/AnantharamanLab/METABOLIC
This software enables the prediction of metabolic and biogeochemical functional trait profiles to any given genome datasets. These genome datasets can either be metagenome-assembled genomes (MAGs), single-cell amplified genomes (SAGs) or pure culture sequenced genomes. It can also calculate the genome coverage. The information is parsed and diagrams for elemental/biogeochemical cycling pathways (currently Nitrogen, Carbon, Sulfur and "other") are produced.
Schematic figure representing major eco-niches of Bathyarchaeota
Phylogenetic tree of bathyarchaeotal 16S rRNA genes (25 subgroups discovered in 2018)
These microbes are able to anaerobically utilize (i) detrital proteins, (ii) polymeric carbohydrates, (iii) fatty acids/aromatic compounds, (iv) methane (or short chain alkane) and methylated compounds, and/or (v) potentially other organic matter. Furthermore, bathyarchaeotal members have wide metabolic capabilities, including acetogenesis, methane metabolism, and dissimilatory nitrogen and sulfur reduction, and they also have potential interactions with anaerobic methane-oxidizing archaea, acetoclastic methanogens and heterotrophic bacteria. (paper link)
Gammaproteobacteria transform organic compounds in deep-sea hydrothermal plumes
”Behind the paper" https://naturemicrobiologycommunity.nature.com/posts/gammaproteobacteria-transform-organic-compounds-in-deep-sea-hydrothermal-plumes
Original publication
B) Community-level microbial and viral ecology and evolution studies
Microbiome and virome encompass the entire genetic information of microbial and viral communities across a variety of spatial and temporal scales. It is of great ecological significance to investigate the community-level functions and interactions of microorganisms and viruses. The outcome of these findings can reveal internal and external networking of the ecosystem, biology and environment interplaying mechanisms, ecology and evolution basis of adaptation strategies, etc. Community-level ecogenomics enable a fine-scale investigation based on genomic blueprints and genome expression activities that can provide quantitative measurements of the diversity, abundance, and activity of microbial and viral players. This approach can lead to fundamental scientific breakthroughs with broad impacts on local and global ecology conservation, environment management, and global climate protection.
We have gained community-level understanding of hydrothermal plume biogeochemistry interactions by investigating data from 37 diverse plumes distributed over eight ocean basins and 206 genomes recovered from three plume ecosystems (in preparation). We discovered that sulfur metabolism defines the core microbiome of hydrothermal plumes and drives metabolic connectivity. The overall ecogenomic analysis on plume environments manifests that the plume microbiome have altered composition, function, genetic structure, and related assistant virome function in better adapt to hydrothermal plume conditions to gain high energy, manage metabolic distribution, and maintain cell activities. Meanwhile, using global-scale ecological genomics and transcriptomics, we have conducted another virus study that reveals the distribution, diversity, activity, evolution, and ecology of virus-associated energy metabolism involving elemental sulfur and thiosulfate oxidation and thiosulfate disproportionation (Nature Communications DOI: 10.1038/s41396-020-00745-5 (2021)) (bioRxiv link). It includes the first reports of SoxC & SoxD in viruses, critical catalytic proteins driving oxidation of thiosulfate in sulfur-oxidizing bacteria. We propose that phage activities are closely coupled to changing geochemistry with higher observed activity in environments with a greater concentration of reduced sulfur compounds. Overall, this study provides novel insights in phage-associated dissimilatory sulfur metabolism and reinforces the necessity of viruses into configurations of metabolism and biogeochemistry.
Conceptual figure indicating the ecology and function of AMGs in sulfur metabolisms.
(a) DSM AMG effect on the budget of reduced sulfur transformation. (b) Diagram of virus-mediated metabolism short circuiting the microbial sulfur loop in nutrient cycling.
C) Single-gene based biogeographic and ecological studies
New microorganisms discovered recently are important players in global carbon and nitrogen cycling; they include anaerobic methanotroph (ANME) and nitrite-dependent anaerobic methane oxidizing (n-damo) bacteria for anaerobic methane oxidation, anaerobic ammonium oxidizing (anammox) bacteria and Thaumarchaeota for nitrogen cycling, and Bathyarchaeota for versatile organics metabolism. Because of their worldwide distribution, knowledge on their diversity and ecological distribution patterns is important to the understanding of their ecophysiological significance. We have used and developed multiple primers in studying their distribution and ecology patterns, such as mcrA, pmoA, nirS (An-nirS & Sc-nirS), hzs, ccs, and nod genes (primer paper link). The functional gene-based biogeographic studies have invented effective and efficient detection and quantification methods, expanded the knowledge of the ocean-terrestrial pattern of anammox and n-damo bacteria, and anthropogenic influences to coasts; and put new insights on their ecological patterns and interactions with environmental factors.
The high-throughput sequencing method-based microbial community studies have discovered the successive transitory distribution of Thaumarchaeota and partitioned distribution of Bathyarchaeota, and niche-differentiation pattern of bacterial community from the Pearl River estuary to the northern South China Sea (nSCS). The distribution patterns of multiple novel microbial groups are unraveled, including: The proportion of Thaumarchaeota in the total archaeal community increased with seawater depth in nSCS. Partitioned distribution of Bathyarchaeota fraction in the whole archaeal community was firstly reported with Subgroups 6 and 8 enriched in shallow-sea sediments. Temperature, seawater depth, and salinity were the three most influential factors correlated with the bacterial communities observed, but comparatively less influential with archaeal communities. Co-existence and co-abundance of marine anammox and n-damo bacteria in deep-sea sediments were observed for the first time. SRBs were enriched in shallow-sea sediments, co-occurring with nitrite-oxidizing Nitrospira and potential sulfide-oxidizing shallow-sea specific JTB255 clade. The global deep-sea cosmopolitans OM1 and deep-sea specific JTB255 clade (newly named as Woeseiaceae) were also of high abundance in deep-sea sediments of nSCS.
Properties of 16S rRNA gene primer and primer pairs on different genera of anammox bacteria deduced by in silico primer evaluation
Phylogenetic tree of 16S rRNA gene and ribosomal proteins of currently defined anammox bacterial species
D) Petroleum reservoir microbiology study
Petroleum reservoir microbes can participate in long-chain fatty acid degradation in situ and convert the intermediates into methane through methanogenic pathways. We observed a high frequency of Thermodesulfovibrio spp., Anaerolineaceae, and Methanoculleus spp. in the long-term (1750 days) incubation of an n-alkane-degrading methanogenic culture. The intermediate metabolites after the initial activation of n-alkanes by fumarate addition reaction could be further degraded by Anaerolineaceae and Thermodesulfovibrio spp., the generalists for intermediate metabolites and Methanoculleus spp. the methane producers that can finally degrade intermediates into small organics, such as acetate, hydrogen, and methyl-compounds, for methane production. In another 13C labeled hexadecane incubation experiment (920 days), the microbial community in the heavy fractions of DNA also showed a significant increase of Anaerolineaceae and Tepidiphilus phylotypes. This study shows the cohort of Anaerolineaceae, Tepidiphilus (firstly discovered their deep involvement of n-alkane degradation this time),and Methanosaeta (acetoclastic methanogen) may play an active role in the hexadecane-degrading based methanogenic process. We have investigated the microbial community of samples from oil/aqueous phases of petroleum reservoirs of different temperatures across China (Biogeosciences, 16, 4229–4241, doi: 10.5194/bg-16-4229-2019 (2019)). The core bacterial microbiome suggest their common functional role in aliphatic and aromatic hydrocarbon degradation across various sites. We discovered community shifting pattern for the first time that the methanogenic process generally shifts from the dominant hydrogenotrophic pathway in the aqueous phase to the acetoclastic pathway in the oil phase in high-temperature reservoirs. The functional profiling indicates the differentiated metabolism of amino acids and hydrocarbons in the oil phase and carbohydrates in the aqueous phase. We summarized the current literature on high-throughput 16S-tag sequencing-based studies on petroleum reservoir microbiome and specifically emphasized methods, applications, recent advances, and future perspectives (in submitting).
Average abundances and functional roles of core bacterial microbiome in all petroleum samples acorss China(including aqueous and oil phase samples) (paper link)