Xiao-Hua Zhang

• Professor at Ocean University of China

Microbial degradation of methylphosphonate (MPn) is an important pathway contributing to the ‘methane paradox’ in the oxic ocean. Vibrio spp. are suggested to participate in this process. However, little is known about the molecular basis, phylogenetic breadth and catabolic efficiency of methane production in Vibrio species. Here, 18 Vibrionales st...

Deep‐sea sediments contain a large number of Thaumarchaeota that are phylogenetically distinct from their pelagic counterparts. However, their ecology and evolutionary adaptations are not well understood. Metagenomic analyses were conducted on samples from various depths of a 750‐cm sediment core collected from the Mariana Trench Challenger Deep. T...

Microbial communities in coastal seas experience strong environmental disturbances, yet their response patterns, especially regarding differently abundant subcommunities, remain poorly understood. Here, through 16S rRNA gene amplicon sequencing, we investigated the diversity, time-decay pattern, and assembly process of abundant, conditionally rare...

Two Gram-stain-negative, facultatively anaerobic, motile, and rod-shaped marine bacteria, designated strains ZSDZ35T and ZSDZ42T, were isolated from surface seawater of Qingdao offshore. Phylogenetic analysis of the 16S rRNA genes and whole genome data placed ZSDZ35T and ZSDZ42T within the genus Enterovibrio. Strain ZSDZ35T was most closely related...

Aquaculture is critical to reduce protein deficiencies and supplement the world’s demand for seafood. However, the culture environment predisposes farmed animals to infectious diseases. In particular, the high density of fish, crustacean, mollusk, sea cucumber or algal species allows for the rapid spread of infectious diseases resulting in devastat...

Coral reefs rely heavily on reef fish for their health, yet overfishing has resulted in their decline, leading to an increase in fast-growing algae and changes in reef ecosystems, a phenomenon described as the phase-shift. A clearer understanding of the intricate interplay between herbivorous, their food, and their gut microbiomes could enhance ree...

Hydrogen sulfide (H2S), methanethiol (MeSH) and dimethylsulfide (DMS) are abundant sulfur gases with roles in biogeochemical cycling, chemotaxis and/or climate regulation. Catabolism of the marine osmolyte dimethylsulfoniopropionate (DMSP) is a major source of DMS and MeSH, but both also result from S-methylation of H2S via MddA, an H2S and MeSH S-...

A Gram–staining–negative, facultative aerobic, motile strain, designated strain ZSDE20T, was isolated from the surface seawater of Qingdao offshore. Phylogenetic analysis of the 16S rRNA gene of strain ZSDE20T, affiliated it to the genus Photobacterium. It was closely related to Photobacterium lutimaris DF-42 T (98.92% 16S rRNA gene sequence simila...

Dimethylsulfoniopropionate (DMSP) is an abundant marine organosulfur compound with roles in stress protection, chemotaxis, nutrient and sulfur cycling and climate regulation. Here we report the discovery of a bifunctional DMSP biosynthesis enzyme, DsyGD, in the transamination pathway of the rhizobacterium Gynuella sunshinyii and some filamentous cy...

The Pollution Nagasaki (PN) section of the East China Sea (ECS) is a typical area for studying the complex hydrographic dynamics between Changjiang River discharge and Kuroshio, displaying intense variations of environmental gradients from nearshore to offshore. However, the temporal and spatial changes of microbial communities along the PN section...

Deep-sea hydrothermal vents have been extensively explored around the globe in the past decades, and the diversity of microbial communities and their ecological functions related to hydrothermal vents have become hotspots in the study of microbial biogeochemistry. However, knowledge of dominant microbial communities and their unique metabolic chara...

Hadal trenches are characterized by enhanced and infrequent high-rate episodic sedimentation events that likely introduce not only labile organic carbon and key nutrients but also new microbes that significantly alter the subseafloor microbiosphere. Currently, the role of high-rate episodic sedimentation in controlling the composition of the hadal...

Methanethiol (MeSH) and dimethyl sulfide (DMS) are important volatile organic sulfur compounds involved in atmospheric chemistry and climate regulation. However, little is known about the metabolism of these compounds in the ubiquitous marine vibrios. Here, we investigated MeSH/DMS production and whether these processes were regulated by quorum-sen...

Dimethylsulfoxonium propionate (DMSOP) is a recently identified and abundant marine organosulfur compound with roles in oxidative stress protection, global carbon and sulfur cycling and, as shown here, potentially in osmotolerance. Microbial DMSOP cleavage yields dimethyl sulfoxide, a ubiquitous marine metabolite, and acrylate, but the enzymes resp...

The world’s deepest yongle blue hole (YBH) is characterized by sharp dissolved oxygen (DO) gradients, and considerably low-organic-carbon and high-inorganic-carbon concentrations that may support active autotrophic communities. To understand metabolic strategies of autotrophic communities for obtaining carbon and energy spanning redox gradients, we...

A Gram-stain-negative, facultative anaerobic, rod-shaped strain, named SDRW27 T , was isolated from offshore seawater collected near Qingdao. Strain SDRW27 T was able to grow at 16–37 °C (optimum, 28 °C), pH 6.0–9.0 (optimum, pH 6.0) and in the presence of 1–7 % (w/v) NaCl (optimum, 3 %). Phylogenetic analysis using 16S rRNA gene sequences indicate...

Background Coral reefs are one of the most biodiverse and productive ecosystems, providing habitat for a vast of species. Reef-building scleractinian corals with a symbiotic microbiome, including bacteria, archaea, viruses and eukaryotic microbes, are referred to coral holobionts. Among them, coral diseases, mainly caused by Vibrio spp., have signi...

Members of the family Vibrionaceae (vibrios) are widely distributed in estuarine, offshore, and marginal seas and perform an important ecological role in the marine organic carbon cycle. Nevertheless, there is little knowledge about whether vibrios play ecological roles in the oligotrophic pelagic area, which occupies a larger water volume. In this...

The Sansha Yongle Blue Hole (SYBH), the deepest blue hole in the world, is an excellent habitat for revealing biogeochemical cycles in the anaerobic environment. However, how sulfur cycling is mediated by microorganisms in the SYBH hasn’t been fully understood. In this study, the water layers of the SYBH were divided into oxic zone, hypoxic zone, a...

Background Hadal trenches (>6000 m) are the deepest oceanic regions on Earth and depocenters for organic materials. However, how these enigmatic microbial ecosystems are fueled is largely unknown, particularly the proportional importance of complex polysaccharides introduced through deposition from the photic surface waters above. In surface waters...

Marine group II (MGII) is the most abundant planktonic heterotrophic archaea in the ocean. The evolutionary history of MGII archaea is elusive. In this study, 13 new MGII metagenome-assembled genomes were recovered from surface to the hadal zone in Challenger Deep of the Mariana Trench; four of them from the deep ocean represent a novel group. The...

Chitin, the most abundant bio-polymer in seawater, may be utilized by various microorganisms as a carbon source. Vibrios have been regarded as one of the main groups of chitin consumers in the marine carbon cycle and chitinase producers. The organisms are widely distributed in the aquatic environment. However, the co-working mechanism between their...

Abstract Microbial lysis of dimethylsulfoniopropionate (DMSP) is a key step in marine organic sulfur cycling and has been recently demonstrated to play an important role in mediating interactions between bacteria, algae, and zooplankton. To date, microbes that have been found to lyse DMSP are largely confined to free‐living and surface‐attached bac...

Coral reefs are among the most biodiverse ecosystems, providing habitats for various organisms. Studies on coral bleaching have been increasing recently, but little is known about the distribution and community assembly of coral pathogenic bacteria (e.g., several Vibrio species). We elucidated the distribution pattern and interaction relationships...

Dimethylsulfoniopropionate (DMSP) and related organic sulfur compounds play key roles in global sulfur cycling. Bacteria have been found to be important DMSP producers in seawater and surface sediments of the aphotic Mariana Trench (MT). However, detailed bacterial DMSP cycling in the Mariana Trench subseafloor remains largely unknown. Here, the ba...

Dimethylsulfoniopropionate (DMSP) is one of the Earth's most abundant organosulfur compounds because many marine algae, bacteria, corals and some plants produce it to high mM intracellular concentrations. In these organisms, DMSP acts an anti-stress molecule with purported roles to protect against salinity, temperature, oxidative stress and hydrost...

Two Gram-stain-negative, facultatively anaerobic, motile, rod-shaped and flagellated marine bacteria, designated strains DBSS07T and ZSDZ65T, were isolated from the surface sediments of the Bohai sea and Qingdao coastal seawater, respectively. Phylogenetic analysis based on 16S rRNA genes, multilocus sequence analysis (MLSA), phylogenomic analysis...

The microbial cycling of dimethylsulfoniopropionate (DMSP) and the resulting gaseous catabolites dimethylsulfide (DMS) or methylmercaptan (MeSH) play key roles in the global sulfur cycle and potentially climate regulation. As the ocean–atmosphere boundary, the sea surface microlayer (SML) is important for the generation and emission of DMS and MeSH...

Quorum sensing (QS) is a chemical communication system by which bacteria coordinate gene expression and social behaviors. Quorum quenching (QQ) refers to processes of inhibiting the QS pathway. Deep-sea hydrothermal vents are extreme marine environments, where abundant and diverse microbial communities live. However, the nature of chemical communic...

Deep ocean blue holes possess steep physicochemical gradients, especially low dissolved oxygen concentration, which shape the extraordinary microbial communities. However, the environmental responses of microorganisms with different lifestyles and knowledge of culturable microorganisms in the blue holes are still unknown. Here, we investigated the...

Two Gram-stain-negative, oxidase-positive, facultative anaerobic and rod-shaped motile bacteria, designated strains ZSDZ34 and ZSDE26, were isolated from offshore surface seawater collected near Qingdao. Phylogenetic analysis based on 16S rRNA gene sequences placed ZSDE26 T and ZSDZ34 T within the genus Vibrio , family Vibrionaceae , class Gammapro...

Alginate is an important carbon source in the marine environment, and vibrios are major alginate utilizers. Previous studies focused only on the characteristics of individual alginate lyases in vibrios, but few of them discussed the comprehensive alginate-degrading strategy.

Vibrio spp. may exert large impacts on biogeochemical cycling in coastal habitats, and their ecological importance has drawn increasing attention. Here, we investigated the spatial distribution pattern and community assembly of Vibrio populations along the Chinese marginal seas, spanning a wide spatial scale.

Site F is the most vigorous cold seep known on the continental slope of the northern South China Sea. Up to now, the microbial community structures in sediments of Site F based on the high-throughput sequencing of the 16S rRNA genes have been studied extensively. However, few studies investigated the microbial community structures at fine vertical...

Microbial seasonality is driven by a set of covarying factors including temperature. There is still a lack of understanding of the details of the phylogenetic structure and susceptibility of microbial communities in response to temperature variation.

Alginate lyases can be used to produce well-defined alginate oligosaccharides (AOSs) because of their specificities for AOS products. A large number of alginate lyases have been recorded in the CAZy database; however, the majority are annotated-only alginate lyases that include little information on their products, thus limiting their applications....

With the development of deep-sea sampling technology, an increasing number of deep-sea Vibrio strains have been isolated, but the adaptation mechanism of these eutrophic Vibrio strains to the deep-sea environment is unclear. Here, our results show that the genome of pelagic Vibrio is streamlined to adapt to a long-term oligotrophic environment.

Background Ubiquitous and diverse marine microorganisms utilise the abundant organosulfur molecule dimethylsulfoniopropionate (DMSP), the main precursor of the climate-active gas dimethylsulfide (DMS), as a source of carbon, sulfur and/or signalling molecules. However, it is currently difficult to discern which microbes actively catabolise DMSP in...

Abstract Marine algae and bacteria produce approximately eight billion tonnes of the organosulfur molecule dimethylsulfoniopropionate (DMSP) in Earth's surface oceans annually. DMSP is an antistress compound and, once released into the environment, a major nutrient, signaling molecule, and source of climate‐active gases. The methionine transaminati...

Halomonas bacteria are ubiquitous in global marine environments, however, their sulfur-oxidizing abilities and survival adaptations in hydrothermal environments are not well understood. In this study, we characterized the sulfur oxidation ability and metabolic mechanisms of Halomonas titanicae SOB56, which was isolated from the sediment of the Tang...

A Gram-stain-negative, non-motile, facultatively anaerobic and non-flagellated marine bacterium, designated JC070 T was isolated from the Yongle Blue Hole in the South China Sea. The temperature, pH and NaCl ranges for growth of strain JC070 T were 4–37 °C (optimum, 16 °C), pH 6.0–9.0 (optimum, pH 7.0) and 1.0 –6.0% (w/v; optimum, 3.0%). The predom...

Background Hadal zone of the deep-sea trenches accommodates microbial life under extreme energy limitations and environmental conditions, such as low temperature, high pressure, and low organic matter down to 11,000 m below sea level. However, microbial pathogenicity, resistance, and adaptation therein remain unknown. Here we used culture-independe...

Antibiotic resistance in gram-negative pathogens has become one of the most serious global public health threats. The role of the N-acyl homoserine lactone (AHL)-mediated signaling pathway, which is widespread in gram-negative bacteria, in the bacterial resistance process should be studied in depth. Here, we report a degrading enzyme of AHLs, MomL,...

Hadal zones are marine environments deeper than 6,000 m, most of which comprise oceanic trenches. Microbes thriving at such depth experience high hydrostatic pressure and low temperature. The genomic potentials of these microbes to such extreme environments are largely unknown. Here, we compare five complete genomes of bacterial strains belonging t...

Dimethylsulfoniopropionate (DMSP) is one of Earth’s most abundant organosulfur molecules, and bacteria in marine sediments have been considered significant producers. However, the vertical profiles of DMSP content and DMSP-producing bacteria in subseafloor sediment have not been described. Here, we used culture-dependent and -independent methods to...

The osmolyte dimethylsulfoniopropionate (DMSP) is produced in petagram amounts by marine microorganisms. Estuaries provide natural gradients in salinity and nutrients, factors known to regulate DMSP production; yet there have been no molecular studies of DMSP production and cycling across these gradients. Here, we study the abundance, distribution...

Metagenomics and metatranscriptomics are powerful methods to uncover key micro-organisms and processes driving biogeochemical cycling in natural ecosystems. Databases dedicated to depicting biogeochemical pathways (for example, metabolism of dimethylsulfoniopropionate (DMSP), which is an abundant organosulfur compound) from metagenomic/metatranscri...

Dimethylsulfoniopropionate (DMSP) is an abundant and ubiquitous organosulfur molecule in marine environments with important roles in global sulfur and nutrient cycling. Diverse DMSP lyases in some algae, bacteria and fungi cleave DMSP to yield gaseous dimethyl sulfide (DMS), an infochemical with important roles in atmospheric chemistry. Here we ide...

Microbial abundance and community composition in marine sediments have been widely explored. However, high-resolution vertical changes of benthic microbial diversity and co-occurrence patterns are poorly described. The ecological contributions of abundant and rare species in sediments also remain largely unknown. Here, by analyzing microbial popula...

Marine algae and bacteria produce eight billion tonnes of the organosulfur molecule dimethylsulfoniopropionate (DMSP) in Earth’s surface oceans every year. DMSP is an anti-stress compound and, once released into the environment, a major nutrient, signalling molecule and source of climate-active gases. The methionine transamination pathway for DMSP...

In a recent Opinion article (‘Viable But Non-Culturable Cells’ are Dead, https://doi.org/10.1111/1462-2920.15463), Song and Wood (2021) argued the cells that can rejuvenate and reconstitute infections are not part of a dormancy continuum. Instead, only persister cells are dormant and capable of re-growth, whereas viable but non-culturable (VBNC) ce...

Increasing macroalgal blooms as a consequence of climate warming and coastal eutrophication have profound effects on the marine environment. The outbreaks of Ulva prolifera in the Yellow Sea of China occurring every summer since 2007 to present have formed the world's largest green tide. The green tide releases huge amounts of dissolved organic mat...

Dimethylsulfoniopropionate (DMSP) is one of Earth’s most abundant organosulfur molecules. Recently, many marine heterotrophic bacteria were shown to produce DMSP, but few studies have combined culture-dependent and independent techniques to study their abundance, distribution, diversity and activity in seawater or sediment environments. Here we inv...

High hydrostatic pressure (HHP) is a characteristic environmental factor of the deep ocean. However, it remains unclear how piezotolerant bacteria adapt to HHP. Here, we identify a two-step metabolic pathway to cope with HHP stress in a piezotolerant bacterium. Myroides profundi D25 T , obtained from a deep-sea sediment, can take up trimethylamine...

A Gram-staining-negative, strictly aerobic, long-rod shaped with no flagellum and yellow-pigmented bacterium designated strain ZXX205 T , was isolated from the hadal seawater at the depth of 7500 m in the Mariana Trench, Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences placed strain ZXX205 T within the genus Winogradskyella and...

Microbial eukaryotes are widespread and play important roles in marine ecosystems. However, their ecological characteristics in the deep sea (>1,000 m), especially hadal trenches, were largely unknown. Here, we investigated the diversity and metabolic potentials of microbial eukaryotes along the whole water column of the Mariana Trench by metagenom...

Quorum sensing (QS) is a density-dependent communicating mechanism that allows bacteria to regulate a wide range of biogeochemical important processes and could be inhibited by quorum quenching (QQ). Increasing researches have demonstrated that QS can affect the degradation of particulate organic matter (POM) in the photic zone. However, knowledge...

Metagenomics and metatranscriptomics are powerful tools to uncover key microbes and processes driving biogeochemical cycling in natural ecosystems. Currently available databases depicting metabolic functions from metagenomic/metatranscriptomic data are not dedicated to biogeochemical cycles. There are no databases encompass genes involved in the cy...

The deepest parts of the world’s oceans hold many mysteries, one of which involves its tiniest residents. Tiny prokaryotes called Thaumarchaeota survive in the extreme environment of the deep oceans. While the metabolic functions of Thaumarchaeota that live in shallower depths are fairly well described, those that live in the deepest sea zone – had...

A Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and non-flagellated marine bacterium strain, designated BOM4T, was isolated from a mussel inhabiting the Tangyin hydrothermal field of the Okinawa Trough. The growth temperature was in the range of 16-40 °C, and the optimum temperature was 37 °C. Optimal growth occurred at pH 7....

Dimethylsulfoniopropionate (DMSP) is an important marine osmolyte. Aphotic environments are only recently being considered as potential contributors to global DMSP production. Here, our Mariana Trench study reveals a typical seawater DMSP/dimethylsulfide (DMS) profile, with highest concentrations in the euphotic zone and decreased but consistent le...

The Earth’s oceans are a huge body of water with physicochemical properties and microbial community profiles that change with depth, which in turn influences their biogeochemical cycling potential. The differences between microbial communities and their functional potential in surface to hadopelagic water samples are only beginning to be explored....

Microbial production and catabolism of dimethylsulfoniopropionate (DMSP), generating the climatically active gases dimethyl sulfide (DMS) and methanethiol (MeSH), have key roles in global carbon and sulfur cycling, chemotaxis, and atmospheric chemistry. Microorganisms in the sea surface microlayer (SML), the interface between seawater and atmospher...

The Mariana Trench in the western North Pacific (NP) contains the deepest (11,000 m) point in the ocean and thus remains the least explored environment. Carbon cycling in the deep Mariana Trench is largely unknown and remains a curious mystery. Here, we report radiocarbon (Δ¹⁴C) and stable carbon isotope (δ¹³C) compositions of dissolved inorganic a...

Vibrio is ubiquitously distributed in marine environments and is the most extensively characterized group within Gammaproteobacteria. Studies have investigated Vibrio spp. worldwide, but mostly focused on pathogenic vibrios and based on cultivation methods. Here, using a combination of molecular and culturing methods, we investigated the dynamics o...

Background: Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans-the hadal zone (depth > 6000 m, consisting al...

A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterium, designated ZYF650T, was isolated from the hadal seawater (9600 m) of the Mariana Trench. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that ZYF650T formed a lineage within the family Alteromonadaceae that was distinct from the most closely re...

Culturing has been the cornerstone of microbiology since Robert Koch first successfully cultured bacteria in the late nineteenth century. However, even today, the majority of microorganisms in the marine environment remain uncultivated. There are various explanations for the inability to culture bacteria in the laboratory, including lack of essenti...

Marine flavobacteria are specialists for polysaccharide degradation. They dominate in habitats enriched with polysaccharides, but are also prevalent in pelagic environments where polysaccharides are less available. These niches are likely occupied by distinct lineages, but evolutionary processes underlying their niche differentiation remain elusive...

The oceans are natural sources of atmospheric methane (CH4), but the origin of excess CH4 at the surface remains enigmatic. Incubation experiments were conducted in the western North Pacific (WNP) and its marginal seas (i.e., Yellow Sea and South China Sea [SCS]) to identify the degradation of methylphosphonate (MPn) to CH4 in the oceans and the mi...

Vibrio harveyi, which belongs to family Vibrionaceae of class Gammaproteobacteria, includes the species V. carchariae and V. trachuri as its junior synonyms. The organism is a well-recognized and serious bacterial pathogen of marine fish and invertebrates, including penaeid shrimp, in aquaculture. Diseased fish may exhibit a range of lesions, inclu...

Background: Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans - the hadal zone (depth > 6,000 m, consisting...