Zhichao Zhou

University of Wisconsin–Madison | UW · Department of Bacteriology

Proteobacteria constitute the most diverse and abundant group of microbes on Earth. In productive marine environments like deep-sea hydrothermal systems, Proteobacteria have been implicated in autotrophy coupled to sulfur, methane, and hydrogen oxidation, sulfate reduction, and denitrification. Beyond chemoautotrophy, little is known about the ecol...

Deep-sea hydrothermal plumes are considered natural laboratories for understanding ecological and biogeochemical interactions. Previous studies focused on interactions between microorganisms and inorganic, reduced hydrothermal inputs including sulfur, hydrogen, iron, and manganese. However, little is known about transformations of organic compounds...

Background: Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capaci...

In globally distributed deep-sea hydrothermal vent plumes, microbiomes are shaped by the redox energy landscapes created by reduced hydrothermal vent fluids mixing with oxidized seawater. Plumes can disperse over thousands of kilometers and their characteristics are determined by geochemical sources from vents, e.g., hydrothermal inputs, nutrients,...

Microbial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs fo...

Viruses are ubiquitous in deep-sea hydrothermal environments, where they exert a major influence on microbial communities and biogeochemistry. Yet, viral ecology and evolution remain understudied in these environments. Here, we identified 49,962 viruses from 52 globally distributed hydrothermal vent samples (10 plumes, 40 deposits, and 2 diffuse fl...

The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophi...

Viruses are ubiquitous in deep-sea hydrothermal environments, where they exert a major influence on microbial communities and biogeochemistry. Yet, viral ecology and evolution remain understudied in these environments. Here, we identified 49,962 viruses from 52 globally distributed hydrothermal vent samples (10 plumes, 40 deposits, and 2 diffuse fl...

Long-term ecological studies are powerful tools to investigate microbiomes and ecosystem change but have mostly ignored viruses. Here, we leveraged a 20-year time-series of a freshwater lake to characterize 1.3 million viral genomes over time, seasonality, and environmental factors. We identified 578 auxiliary metabolic gene (AMG) clusters represen...

Hydrothermal plumes are deep-sea extreme environments that support dynamic microbial metabolisms. Chemoautotrophic production coupled to the oxidation of reduced energy-laden substrates has been considered the primary metabolism in plumes. Recently, sequencing data suggested organic carbon cycling may also be important. However, the biogeochemical...

Long-term ecological studies are powerful tools to investigate microbiomes and ecosystem change but have mostly ignored viruses. Here, we leveraged a 20-year time-series of a freshwater lake to characterize 1.3 million viral genomes over time, seasonality, and environmental factors. We identified 578 auxiliary metabolic gene (AMG) clusters represen...

Single-cell genetic heterogeneity is ubiquitous in microbial populations and an important aspect of microbial biology; however, we lack a broadly applicable and accessible method to study this heterogeneity in microbial populations. Here, we show a simple, robust and generalizable method for high-throughput single-cell sequencing of target genetic...

Viruses are increasingly being recognized as important components of human and environmental microbiomes. However, viruses in microbiomes remain difficult to study because of the difficulty in culturing them and the lack of sufficient model systems. As a result, computational methods for identifying and analyzing uncultivated viral genomes from met...

Deep-sea hydrothermal vents are abundant on the ocean floor and play important roles in ocean biogeochemistry. In vent ecosystems such as hydrothermal plumes, microorganisms rely on reduced chemicals and gases in hydrothermal fluids to fuel primary production and form diverse and complex microbial communities. However, microbial interactions that d...

Viruses are increasingly being recognized as important components of human and environmental microbiomes. However, viruses in microbiomes remain difficult to study because of difficulty in culturing them and the lack of sufficient model systems. As a result, computational methods for identifying and analyzing uncultivated viral genomes from metagen...

The molecular and ecological factors shaping horizontal gene transfer (HGT) via natural transformation in microbial communities are largely unknown, which is critical for understanding the emergence of antibiotic-resistant pathogens. We investigate key factors shaping HGT in a microbial co-culture by quantifying extracellular DNA release, species g...

The arginine dihydrolase metabolic pathway (arc operon) is present in the genomes of diverse human gut bacterial species and can modulate environmental pH. We lack an understanding of the role of this pathway on community-level interactions. We investigated the role of the arc operon in the probiotic E. coli Nissle on the assembly and production of...

Background When deep-sea hydrothermal fluids mix with cold oxygenated fluids, minerals precipitate out of solution and form hydrothermal deposits. These actively venting deep-sea hydrothermal deposits support a rich diversity of thermophilic microorganisms which are involved in a range of carbon, sulfur, nitrogen, and hydrogen metabolisms. Global p...

The division of organisms on the Tree of Life into either a three-domain (3D) tree or a two-domain (2D) tree has been disputed for a long time. Ever since the discovery of Archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as the evolutionary marker, there has been a great advance in our knowledge of not only the growing diversity of Ar...

Single cell genetic heterogeneity is ubiquitous in microbial populations and an important aspect of microbial biology. However, we lack a broadly applicable and accessible method to study this heterogeneity at the single cell level. Here, we introduce a simple, robust, and generalizable platform for quantitative and massively parallel single cell s...

Deep sea hydrothermal vents are abundant on the ocean floor and play important roles in ocean biogeochemistry. In vent ecosystems such as hydrothermal plumes, microorganisms rely on reduced chemicals and gases in hydrothermal fluids to fuel primary production and form diverse and complex microbial communities. However, microbial interactions that d...

Mangrove wetland is one of the most important ecosystems along the coast and often suffers from global climate change as well as the anthropogenic activities. Nitrite-dependent anaerobic methane oxidization (n-damo) bacteria play an important role in linking the microbial geochemical cycles of carbon and nitrogen in the wetlands, but the pattern of...

Microbial nitrite-dependent anaerobic methane oxidation (n-damo) process is important for mitigating methane emission and anthropogenic nitrogen inputs in the marine environment. However, the distribution pattern of n-damo bacteria along an anthropogenic N-input gradient from the coastal wetland to the pristine South China Sea is poorly understood....

Background When deep-sea hydrothermal fluids mix with cold oxygenated fluids, minerals precipitate out of solution and form hydrothermal deposits. These actively venting deep-sea hydrothermal vent deposits support a rich diversity of thermophilic microorganisms which are involved in a range of carbon, sulfur, nitrogen, and hydrogen metabolisms. Glo...

Background When deep-sea hydrothermal fluids mix with cold oxygenated fluids, minerals precipitate out of solution and form hydrothermal deposits. These actively venting deep-sea hydrothermal vent deposits support a rich diversity of thermophilic microorganisms which are involved in a range of carbon, sulfur, nitrogen, and hydrogen metabolisms. Glo...

In globally distributed deep-sea hydrothermal vent plumes, microbiomes are shaped by the redox energy landscapes created by reduced hydrothermal vent fluids mixing with oxidized seawater. Plumes can disperse over thousands of kilometers and are complex. Their characteristics are determined by geochemical sources from hydrothermal vents, e.g., hydro...

Studies on marine bacterial communities have revealed endemism in local communities, yet the underlying mechanisms remained elusive. Environmental gradient settings can benefit the straightaway study of community composition changes and the mechanisms explaining them. Here, MiSeq-based 16S rRNA gene sequencing was performed on 12 surface sediment s...

Background Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacit...

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...

Polysaccharide utilization loci (PULs) are co-regulated bacterial genes that sense nutrients and enable glycan digestion. Human gut microbiome members, notably Bacteroides, contain numerous PULs that enable glycan utilization and shape ecological dynamics. To investigate the role of PULs on fitness and inter-species interactions, we develop a CRISP...

Background: Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capaci...

Viruses influence the fate of nutrients and human health by killing microorganisms and altering metabolic processes. Organosulfur metabolism and biologically derived hydrogen sulfide play dynamic roles in manifestation of diseases, infrastructure degradation, and essential biological processes. Although microbial organosulfur metabolism is well stu...

Polysaccharide utilization loci (PULs) in the human gut microbiome have critical roles in shaping human health and ecological dynamics. We develop a CRISPR-FnCpf1-RecT genome-editing tool to study 23 PULs in the highly abundant species B. uniformis (BU). We identify the glycan-degrading functions of multiple PULs and elucidate transcriptional coord...

Asgard is a recently discovered archaeal superphylum, closely linked to the emergence of eukaryotes. Among Asgard archaea, Lokiarchaeota are abundant in marine sediments, but their in situ activities are largely unknown except for Candidatus 'Prometheoarchaeum syntrophicum'. Here, we tracked the activity of Lokiarchaeota in incubations with Helgola...

Viruses influence the fate of nutrients and human health by killing microorganisms and altering metabolic processes. Organosulfur metabolism and biologically-derived hydrogen sulfide play dynamic roles in manifestation of diseases, infrastructure degradation, and essential biological processes. While microbial organosulfur metabolism is well-studie...

Anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) processes are two newly discovered biochemical pathways for removal of reactive nitrogen species and methane. An investigation was initiated to investigate the simultaneous removal of ammonium and methane and the corresponding microorganisms in a full-...

Polymer composites are attractive for structural applications in the built environment due to their lightweight and high strength properties but suffer from degradation due to environmental factors. While abiotic factors like temperature, moisture, and ultraviolet light are well studied, little is known about the impacts of naturally occurring micr...

Asgard is a recently discovered archaeal superphylum, closely linked to the emergence of eukaryotes. Among Asgard archaea, Lokiarchaeota are abundant in marine sediments, but their in situ activities are largely unknown except for Candidatus 'Prometheoarchaeum syntrophicum'. Here, we tracked the activity of Lokiarchaeota in incubations with Helgola...

Microbial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs fo...

Microbial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs fo...

The proinflammatory and genotoxic properties of hydrogen sulfide (H2S) have been implicated as an environmental trigger of colonic disease. Recent evidence links sulfidogenic bacteria capable of metabolizing organic sulfur substrates, like dietary sulfur amino acids and taurine conjugated bile acids, with increased colorectal cancer (CRC) and colit...

Background Mangroves are highly productive ecosystems, with one of the highest microbial diversities among all ecosystems. The concerted activity of microbial community in mangrove sediment mediates element cycling, but the underpinning mechanism of microbial synergy remains unknown. Results Here, we reconstructed 671 strain-resolved metagenome-ass...

Bathyarchaeota is a newly proposed phylum of archaeal organisms. Its diverse members inhabit anoxic environments such as hot springs, salt marshes, mangrove sediments, and the sub-seafloor. While Bathyarchaeota is believed to be an important driver of the global carbon cycle, little is known about the phylum's true metabolic potential. A new study...

Viruses that infect bacteria and archaea are abundant in human and environmental microbiomes. Their roles in manipulating, killing, and recycling microbes makes them key players in environmental processes and human health and disease, including inflammatory bowel diseases. In spite of their importance, the tools available for analyzing viral genome...

Background: Viruses are central to microbial community structure in all environments. The ability to generate large metagenomic assemblies of mixed microbial and viral sequences provides the opportunity to tease apart complex microbiome dynamics, but these analyses are currently limited by the tools available for analyses of viral genomes and asse...

Proteobacteria constitute one of the most diverse and abundant groups of microbes on Earth. In productive marine environments like deep-sea hydrothermal systems, Proteobacteria are implicated in autotrophy coupled to sulfur, methane, and hydrogen oxidation, sulfate reduction, and denitrification. Beyond chemoautotrophy, little is known about the ec...

Polymer composites have become attractive for structural applications in the built environment due to their lightweight and high strength properties but can suffer from degradation due to environmental factors. While impacts of abiotic factors like temperature and moisture are well studied, little is known about the influence of naturally occurring...

Functional genes, namely hzo/hao, nirS, hzs, and ccs gene, are efficient with high specificity for detecting anammox bacteria. Sc-nirS and An-nirS primer sets were proposed for targeting Scalindua/non-Scalindua anammox bacterial groups; previously, they have not been assessed for biogeographic study on marine-terrestrial transitional systems, speci...

Background: Bathyarchaeota, a newly proposed archaeal phylum, is considered as an important driver of the global carbon cycle. However, due to the great diversity of them, there is limited genomic information that accurately encompasses the metabolic potential of the entire archaeal phylum. Results: In the current study, nine metagenome-assemble...

Background: Viruses are central to microbial community structure in all environments. The ability to generate large metagenomic assemblies of mixed microbial and viral sequences provides the opportunity to tease apart complex microbiome dynamics, but these analyses are currently limited by the tools available for analyses of viral genomes and asses...

Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the...

This study provides comprehensive metabolic insights into the Hydrothermarchaeota from comparative genomics, evolution, and community-level perspectives. Members of the Hydrothermarchaeota synergistically participate in a wide range of carbon-utilizing and element cycling processes with other microorganisms in the community. We expand the current u...

Background Viruses are central to microbial community structure in all environments. The ability to generate large metagenomic assemblies of mixed microbial and viral sequences provides the opportunity to tease apart complex microbiome dynamics, but these analyses are currently limited by the tools available for analyses of viral genomes and assess...

Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes (MAGs) from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named...

Background Viruses are central to microbial community structure in all environments. The ability to generate large metagenomic assemblies of mixed microbial and viral sequences provides the opportunity to tease apart complex microbiome dynamics, but these analyses are currently limited by the tools available for analyses of viral genomes and assess...

Microorganisms in petroleum reservoirs play significant roles in hydrocarbon degradation, and through the terminal electron-accepting process of methanogenesis, they also contribute to microbially enhanced oil recovery (MEOR) worldwide, with great economic and environmental benefits. Here, a molecular investigation, using the 16S rRNA and mcrA gene...

Hydrothermal vents release reduced compounds and small organic carbons into surrounding seawaters, providing essential substrates for microbial-derived biosynthesis and bioenergy transformations. Despite the wide distribution of Marine Benthic Group-E archaea (referred to as Hydrothermarchaeota) in hydrothermal environments, little is known on thei...

Microbial metabolism mediates fundamental transformations of chemistry and energy that drive biogeochemical cycles on our planet. Increasingly, we can read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes using omic-based techniques such as metagenomic...

Revealing the diversity and distribution of archaea is basically crucial to understanding their ecological functions in subsurface petroleum reservoir ecosystems. However, the knowledge about the abundance and distribution of new archaea in such environments is still limited. In the present work, archaeal communities from five production wells of a...

Free‐living and particle‐associated microbial communities play critical roles in nutrient cycles in aquatic systems. However, little is known about their assembly process, function, and interactions. Here, by using 16S rRNA gene amplicon sequencing of size‐fractionated samples collected during the wet and dry seasons, we investigated the assembly p...

Microbial nitrogen removal mediated by anaerobic ammonium oxidation (anammox) are cost-effective, yet it is time-consuming to accumulate the slow-growing anammox bacteria in conventional wastewater treatment plants (WWTPs). Inoculation of anammox enriched pellets is an effective way to establish anammox and achieve shortcut nitrogen removal in full...

Microbial nitric oxide dismutation reaction (NOD), involved in the biogeochemical nitrogen cycle on Earth, has been implemented to N removal in laboratory-scale wastewater treatment systems, but microorganisms from relatively a few lineages have been implicated to be associated with this biochemical process. Detection of abundant putative (or novel...

Methanogenic biodegradation of n-alkanes is an important process in the biogeochemical carbon cycles. The key players in this biochemical processes were investigated for a 920-day of culturing with universally labelled (UL)-¹³C-hexadecane and 1, 2-¹³C-hexadecane as the sources of carbon and energy, using stable isotope probing combined with 16S rRN...

Microorganisms in petroleum reservoirs mediate hydrocarbon degradation coupling with methanogenesis process as the terminal step, they also contribute to microbial enhanced oil recovery (MEOR) worldwide with great economic and environmental benefits. Here, a molecular investigation, using the 16S rRNA and mcrA gene profiles based on MiSeq sequencin...

Bathyarchaeota is a diverse, abundant, and widespread archaeal phylum that may play an important role in global carbon cycling. The vertical distribution of Bathyarchaeota and environmental impact on bathyarchaeotal community in deep-sea and lake sediments are known; however, little information is available on Bathyarchaeota in eutrophic and bracki...