Rare subcommunity maintains the stability of ecosystem multifunctionality by deterministic assembly processes in subtropical estuaries.

Microorganisms, especially rare microbial species, are crucial in estuarine ecosystems for driving biogeochemical processes and preserving biodiversity. However, the understanding of the links between ecosystem multifunctionality (EMF) and the diversity of rare bacterial taxa in estuary ecosystems remains limited. Employing high-throughput sequencing and a variety of statistical methods, we assessed the diversities and assembly process of abundant and rare bacterioplankton and their contributions to EMF in a subtropical estuary. Taxonomic analysis revealed Proteobacteria as the predominant phylum among both abundant and rare bacterial taxa. Notably, rare taxa demonstrated significantly higher taxonomic diversity and a larger species pool than abundant taxa. Additionally, our findings highlighted that deterministic assembly processes predominantly shape microbial communities, with heterogeneous selection exerting a stronger influence on rare taxa. Further analysis reveals that rare bacterial beta-diversity significantly impacts to EMF, whereas alpha diversity did not. The partial least squares path modeling (PLS-PM) analysis demonstrated that the beta diversity of abundant and rare taxa, as the main biotic factor, directly affected EMF, while temperature and total organic carbon (TOC) were additional key factors to determine the relationship between beta diversity and EMF. These findings advance our understanding of the distribution features and ecological knowledge of the abundant and rare taxa in EMF in subtropical estuaries, and provide a reference for exploring the multifunctionality of different biospheres in aquatic environments.

Resource diversity disturbs marine Vibrio diversity and community stability, but loss of Vibrio diversity enhances community stability.

Vibrio is a salt-tolerant heterotrophic bacterium that occupies an important ecological niche in marine environments. However, little is known about the contribution of resource diversity to the marine Vibrio diversity and community stability. In this study, we investigated the association among resource diversity, taxonomic diversity, phylogenetic diversity, and community stability of marine Vibrio in the Beibu Gulf. V. campbellii and V. hangzhouensis were the dominant groups in seawater and sediments, respectively, in the Beibu Gulf. Higher alpha diversity was observed in the sediments than in the seawater. Marine Vibrio community assembly was dominated by deterministic processes. Pearson's correlation analysis showed that nitrite (NO2--N), dissolved inorganic nitrogen (DIN), ammonium (NH4+-N), and pH were the main factors affecting marine Vibrio community stability in the surface, middle, and bottom layers of seawater and sediment, respectively. Partial least-squares path models (PLS-PM) demonstrated that resource diversity, water properties, nutrients, and geographical distance had important impacts on phylogenetic and taxonomic diversity. Regression analysis revealed that the impact of resource diversity on marine Vibrio diversity and community stability varied across different habitats, but loss of Vibrio diversity increases community stability. Overall, this study provided insights into the mechanisms underlying the maintenance of Vibrio diversity and community stability in marine environments.

Disentangling the Ecological Processes and Driving Forces Shaping the Seasonal Pattern of Halobacteriovorax Communities in a Subtropical Estuary.

Halobacteriovorax are predatory bacteria that have a significant ecological role in marine environments. However, understanding of dynamics of populations, driving forces, and community composition of Halobacteriovorax groups in natural marine environments is still limited. Here, we used high-throughput sequencing to study the underlying mechanisms governing the diversity and assembly of the Halobacteriovorax community at spatiotemporal scales in a subtropical estuary. Phylogenetic analysis showed that 10 of 15 known Halobacteriovorax clusters were found in the studied estuary. Halobacteriovorax α-diversity and ß-diversity exhibited significant seasonal variation. Variation partitioning analysis showed that the effect of nutrients was greater than that of other measured water properties on Halobacteriovorax community distribution. The results of Spearman's and Mantel's tests indicated that the trophic pollutants dissolved inorganic phosphorus (DIP) and NH4+-N in the estuary were the key factors that significantly affected Halobacteriovorax species and community diversity. In addition, this work indicated that the biological stoichiometry (especially N/P) of nutrients exerted a significant influence on the Halobacteriovorax community. Furthermore, we found that both deterministic and stochastic processes contributed to the turnover of Halobacteriovorax communities, and environmental filtering dominated the assembly of estuarine Halobacteriovorax communities. Overall, we provide new insights into the mechanisms in the generation and maintenance of the Halobacteriovorax community in marine environments.

Abundant and Rare Taxa of Planktonic Fungal Community Exhibit Distinct Assembly Patterns Along Coastal Eutrophication Gradient.

Revealing planktonic fungal ecology under coastal eutrophication is crucial to our understanding of microbial community shift in marine pollution background. We investigated the diversity, putative interspecies interactions, assembly processes and environmental responses of abundant and rare planktonic fungal communities along a eutrophication gradient present in the Beibu Gulf. The results showed that Dothideomycetes and Agaricomycetes were the predominant classes of abundant and rare fungi, respectively. We found that eutrophication significantly altered the planktonic fungal communities and affected the abundant taxa more than the rare taxa. The abundant and rare taxa were keystone members in the co-occurrence networks, and their interaction was enhanced with increasing nutrient concentrations. Stochastic processes dominated the community assembly of both abundant and rare planktonic fungi across the eutrophication gradient. Heterogeneous selection affected abundant taxa more than rare taxa, whereas homogenizing dispersal had a greater influence on rare taxa. Influences of environmental factors involving selection processes were detected, we found that abundant fungi were mainly influenced by carbon compounds, whereas rare taxa were simultaneously affected by carbon, nitrogen and phosphorus compounds in the Beibu Gulf. Overall, these findings highlight the distinct ecological adaptations of abundant and rare fungal communities to marine eutrophication.

Climate and nutrients regulate biographical patterns and health risks of antibiotic resistance genes in mangrove environment.

Mangroves are prone to receive pollutants and act as a sink for antibiotic resistance genes (ARGs). However, knowledge of the human health risk of ARGs and its influencing factors in mangrove ecosystems is limited, particularly at large scales. Here, we applied a high-throughput sequencing technique combined with an ARG risk assessment framework to investigate the profiles of ARGs and their public health risks from mangrove wetlands across South China. We detected 456 ARG subtypes, and found 71 of them were identified as high-risk ARGs, accounting for 0.25 % of the total ARG abundance. Both ARGs and bacterial communities showed a distance-decay biogeography, but ARGs had a steeper slope. Linear regression analysis between features of co-occurrence network and high-risk ARG abundance implies that greater connections in the network would result in higher health risk. Structural equation models showed that geographic distance and MGEs were the most influential factors that affected ARG patterns, ARGs and MGEs contributed the most to the health risk profiles in mangrove ecosystems. This work provides a novel understanding of biogeographic patterns and health risk assessment of ARGs in mangrove ecosystems and can have profound significance for mangrove environment management with regard to ARG risk control.

Ecological stoichiometry influences phytoplankton alpha and beta diversity rather than the community stability in subtropical bay.

Numerous studies have shown that changes in environmental factors can significantly impact and shift the structure of phytoplankton communities in marine ecosystems. However, little is known about the association between the ecological stoichiometry of seawater nutrients and phytoplankton community diversity and stability in subtropical bays. Therefore, we investigated the relationship between the phytoplankton community assemblage and seasonal variation in the Beibu Gulf, South China Sea. In this study, we found that the abundance of Bacillariophyceae in spring was relatively greater than in other seasons, whereas the abundance of Coscinodiscophyceae was relatively low in spring and winter but greatly increased in summer and autumn. Values of the alpha diversity indices gradually increased from spring to winter, revealing that seasonal variations shifted the phytoplankton community structure. The regression lines between the average variation degree and the Shannon index and Bray-Curtis dissimilarity values showed significantly positive correlations, indicating that high diversity was beneficial to maintaining community stability. In addition, the ecological stoichiometry of nutrients exhibited significantly positive associations with Shannon index and Bray-Curtis dissimilarity, demonstrating that ecological stoichiometry can significantly influence the alpha and beta diversity of phytoplankton communities. The C:N:P ratio was not statistically significantly correlated with average variation degree, suggesting that ecological stoichiometry rarely impacted the community stability. Temperature, nitrate, dissolved inorganic phosphorous, and total dissolved phosphorus were the main drivers of the phytoplankton community assemblage. The results of this study provide new perspectives about what influences phytoplankton community structure and the association between ecological stoichiometry, community diversity, and stability in response to environmental changes.

Trophic states regulate assembly processes and network structures of small chromophytic phytoplankton communities in estuarine and coastal ecosystem.

Small chromophytic phytoplankton (SCP) are anticipated to be more important for a significant proportion of primary production in estuarine-coastal ecosystems. However, responses of SCP community to coastal eutrophication are still unclear. In this study, we investigated diversity, co-occurrence and assembly features of SCP communities, as well as relationship with environmental factors in subtropical Beibu Gulf. The results exhibited that the alpha diversity and beta diversity of SCP communities were significantly different among eutrophic states. Co-occurrence network revealed a complex interaction that most amplicon sequence variants (ASVs) in modules of the network were specific to trophic states. Further, phylogenetic based ß-nearest taxon distance analyses revealed that stochastic processes mainly provided 69.26% contribution to SCP community assembly, whereas deterministic processes dominated community assembly in heavy eutrophic state. Overall, our findings elucidate the mechanism of diversity and assembly in SCP community and promote the understanding of SCP ecology related to subtropical coastal eutrophication.

Co-occurrence of chromophytic phytoplankton and the Vibrio community during Phaeocystis globosa blooms in the Beibu Gulf.

Accumulating research evidence has revealed that harmful algal blooms (HABs) can substantially affect the community structures of phytoplankton and heterotrophic bacteria in marine ecosystems. However, little is known about their species-specific interactions between phytoplankton and heterotrophic bacteria during the HABs period and about their interaction shifts in response to blooms. From this perspective, we investigated the co-occurrence of chromophytic phytoplankton and Vibrio during Phaeocystis globosa blooms in the Beibu Gulf. The results showed that Vibrio communities were distinct during the blooms, and P. globosa blooms resulted in a decline in phytoplankton alpha diversity, revealing that the blooms could affect their community compositions. The regression lines between the Shannon indices and Bray-Curtis distances of phytoplankton and Vibrio showed positive correlations with each other (p < 0.001), suggesting that they may have intrageneric symbiotic interactions overall. In addition, network analysis further demonstrated that relationships between phytoplankton and Vibrio were dominated by positive correlations, and more interaction modules were observed during the blooms, revealing that the blooms intensified synergistic association and mutual symbiotic interactions between them. Environmental factors (SiO32-, NH4+, NO3- and TN,) and P. globosa density more deeply affected network interactions between phytoplankton and Vibrio during the periods of P. globosa blooms than those before the blooms and after the blooms. This study provided new insight to elucidate community structure and interaction relationships between phytoplankton and Vibrio in response to P. globosa blooms and their ecological effects in marine ecosystems.

Responses of Free-Living Vibrio Community to Seasonal Environmental Variation in a Subtropical Inland Bay.

Vibrio are widely distributed in aquatic environments and strongly associated with eutrophic environments and human health through the consumption of contaminated seafood. However, the response of the Vibrio community to seasonal variation in eutrophic environments is poorly understood. In this study, we used a Vibrio-specific 16S rRNA sequencing approach to reveal the seasonal distribution pattern and diversity of the Vibrio community in the Maowei Sea, Beibu Gulf of China. The Shannon diversity of the Vibrio community was highest in the summer, while ß-diversity analysis showed that Vibrio community structures were significantly different between seasons. Distance-based redundancy analysis (dbRDA) and Mantel test analysis suggested that total dissolved nitrogen (TDN), total dissolved phosphorus (TDP), dissolved inorganic nitrogen (DIN), salinity, and temperature were the key environmental factors shaping the Vibrio community structure, indicating a strong filtering effect of trophic condition on Vibrio communities. Furthermore, through random forest analysis, V. fluvialis, V. alginolyticus, V. proteolyticus, V. splendidus, and the other eight Vibrio species were more sensitive to eutrophic changes. This study revealed seasonal changes in Vibrio communities and the influence of environmental variation on Vibrio community composition, contributing to a better understanding of their potential ecological roles in a subtropical inland bay.

Patterns and drivers of Vibrio isolates phylogenetic diversity in the Beibu Gulf, China.

Members of the genus Vibrio are ubiquitous in aquatic environments and can be found either in a culturable or a viable but nonculturable (VBNC) state. Despite widespread concerns as to how to define the occurrence and dynamics of Vibrio populations by culture-independent approaches, further physiological research and relevant biotechnological developments will require the isolation and cultivation of the microbes from various environments. The present work provides data and perspectives on our understanding of culturable Vibrio community structure and diversity in the Beibu Gulf. Finally, we isolated 1,037 strains of Vibrio from 45 samples and identified 18 different species. Vibrio alginolyticus, V. cyclitrophicus, V. tasmaniensis, V. brasiliensis, and V. splendidus were the dominant species that had regional distribution characteristics. The correlation between the quantitative distribution and community structure of culturable Vibrio and environmental factors varied with the Vibrio species and geographical locations. Among them, salinity, nitrogen, and phosphorus were the main factors affecting the diversity of culturable Vibrio. These results help to fill a knowledge gap on Vibrio diversity and provide data for predicting and controlling pathogenic Vibrio outbreaks in the Beibu Gulf.

Spatial distribution and functional profile of the bacterial community in response to eutrophication in the subtropical Beibu Gulf, China.

In this study, we investigated the specific bacterial distribution and the response of bacterial communities to shifts in environmental factors in the subtropical Beibu Gulf, southern China. The abundances of Actinobacteria, Bacilli, Planctomycetia, Thermoleophilia, Anaerolineae, and Synechococcophycideae were significantly higher in high eutrophic samples than in medium eutrophic and oligotrophic samples. Bacterial alpha-diversity was found greater in high eutrophication samples than in the other samples. Besides, Ponticaulis koreensis, Nautella italic, Anaerospora hongkongensis, Candidatus Aquiluna rubra, and Roseovarius pacificus were sensitive to trophic variation and thus could be used as eco-markers. In addition, the relative abundances of functional genes involving carbohydrate and amino acid metabolism were very high among the samples. We also found temperature, Chl-a, TDN and NO3- were the main environmental drivers of bacterial community structure. Overall, this study provides new insight into the composition of bacterial community and function response to gradients of eutrophication in Beibu Gulf.

Stochastic processes dominate marine free-living Vibrio community assembly in a subtropical gulf.

Understanding the effects of eutrophication on heterotrophic bacteria, a primary responder to eutrophication, is critical for predicting the responses of ecosystems to marine environmental pollution. Vibrio are indigenous in coastal water and of significance to geochemical cycling and public health. In this study, we investigated the diversity and assembly features of Vibrio, as well as their relationship with the environmental factors in the subtropical Beibu Gulf. We found that the alpha diversity of Vibrio increased in parallel with the trophic state they occupy. A Mantel test indicated that the trophic state was correlated to Vibrio beta diversity and the correlation gradually strengthened at higher trophic states. Variation partitioning analysis suggested that the geographic distance was an important factor impacting the variables of Vibrio communities in all the samples, but nutrients exerted more influence in the more highly eutrophic samples. Our results demonstrated that stochastic processes govern the turnover of marine Vibrio communities in the Beibu Gulf and that ecological drift was the most important process for assembly of the Vibrio communities.

Phylogenetic Responses of Marine Free-Living Bacterial Community to Phaeocystis globosa Bloom in Beibu Gulf, China.

Phaeocystis globosa blooms are recognized as playing an essential role in shaping the structure of the marine community and its functions in marine ecosystems. In this study, we observed variation in the alpha diversity and composition of marine free-living bacteria during P. globosa blooms and identified key microbial community assembly patterns during the blooms. The results showed that the Shannon index was higher before the blooming of P. globosa in the subtropical bay. Marinobacterium (γ-proteobacteria), Erythrobacter (α-proteobacteria), and Persicobacter (Cytophagales) were defined as the most important genera, and they were more correlated with environmental factors at the terminal stage of P. globosa blooms. Furthermore, different community assembly processes were observed. Both the mean nearest relatedness index (NRI) and nearest taxon index (NTI) revealed the dominance of deterministic factors in the non-blooming and blooming periods of P. globosa, while the bacterial communities in marine waters after the blooms tended to be controlled by stochastic factors. Our findings revealed that the assembly of the bacterial community in marine P. globosa blooms is a complex process with mixture effects of marine microbiomes and environmental parameters.

Prevalence and proliferation of antibiotic resistance genes in the subtropical mangrove wetland ecosystem of South China Sea.

The emerging pollutants antibiotic resistance genes (ARGs) are prevalent in aquatic environments such as estuary. Coastal mangrove ecosystems always serve as natural wetlands for receiving sewage which always carry ARGs. Currently, the research considering ARG distribution in mangrove ecosystems gains more interest. In this work, we investigated the diversity of ARGs in an urban estuary containing mangrove and nonmangrove areas of the South China Sea. A total of 163 ARGs that classified into 22 resistance types and six resistance mechanisms were found. ARG abundance of the samples in the estuary is between 0.144 and 0.203. This is within the general range of Chinese estuaries. The difference analysis showed that abundances of total ARGs, six most abundant ARGs (mtrA, rpoB, rpoC, rpsL, ef-Tu, and parY), the most abundant resistance types (elfamycin, multidrug, and peptide), and the most abundant resistance mechanism (target alteration) were significantly lower in mangrove sediment than that in nonmangrove sediment (p < 0.05). Network and partial redundancy analysis showed that sediment properties and mobile genetic elements were the most influential factors impacting ARG distribution rather than microbial community. The two factors collectively explain 51.22% of the differences of ARG distribution. Our study indicated that mangrove sediments have the capacity to remove ARGs. This work provides a research paradigm for analysis of ARG prevalence and proliferation in the subtropical marine coastal mangrove ecosystem.

Carbohydrate metabolism genes dominant in a subtropical marine mangrove ecosystem revealed by metagenomics analysis.

Mangrove sediment microorganisms play a vital role in the energy transformation and element cycling in marine wetland ecosystems. Using metagenomics analysis strategy, we compared the taxonomic structure and gene profile of the mangrove and non-mangrove sediment samples at the subtropical estuary in Beibu Gulf, South China Sea. Proteobacteria, Bacteroidetes, and Firmicutes were the most abundant bacterial phyla. Archaeal family Methanosarcinaceae and bacterial genera Vibrio and Dehalococcoides were significantly higher in the mangrove sediments than in the nonmangrove sediments. Functional analysis showed that "Carbohydrate metabolism" was the most abundant metabolic category. The feature of carbohydrate-active enzymes (CZs) was analyzed using the Carbohydrate-Active EnZymes Database. The significant differences of CZs between mangrove and non-mangrove sediments, were attributed to the amounts of polyphenol oxidase (EC 1.10.3.-), hexosyltransferase (EC 2.4.1.-), and ß-N-acetylhexosaminidase (EC 3.2.1.52), which were higher in the mangrove sediment samples. Principal component analysis indicated that the microbial community and gene profile between mangrove and non-mangrove sediments were distinct. Redundancy analysis showed that total organic carbon is a significant factor that affects the microbial community and gene distribution. The results indicated that the mangrove ecosystem with massive amounts of organic carbon may promote the richness of carbohydrate metabolism genes and enhance the degradation and utilization of carbohydrates in the mangrove sediments.

Isolation and biochemical characterization of a metagenome-derived 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase gene from subtropical marine mangrove wetland sediments.

3-Deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) is a key rate-limiting enzyme in aromatic amino acid anabolism. A new Iß-type DAHPS gene (aro1A) was identified in a metagenomic library from subtropical marine mangrove sediment. The gene encoded a polypeptide composed of 272 amino acids and had a maximum similarity of 52.4% to a known DAHPS at the amino acid level. Multiple sequence alignment, homologous modeling, and molecular docking showed that Aro1A had the typical (ß/α)8 barrel-shaped catalytic structural domain of DAHPS. The motifs and amino acid residues involved in the combination of substrates and metal ligand were highly conservative with the known DAHPS. The putative DAHPS gene was subcloned into a pET-30a(+) vector and was overexpressed in Escherichia coli Rosetta (DE3) cells. The recombinant protein was purified to homogeneity. The maximum activity for the recombinant Aro1A protein occurred at pH 8.0 and 40 °C. Ba2+ and Ca2+ stimulated the activity of Aro1A protein. The enzyme showed high affinity and catalytic efficiency (K m PEP = 19.58 µM, V max PEP = 29.02 µM min-1, and k cat PEP /K m PEP = 0.88 s-1 µM-1) under optimal reaction conditions. The enzymatic property of Aro1A indicates its potential in aromatic amino acid industrial production.

Identification and molecular characterization of a metagenome-derived L-lysine decarboxylase gene from subtropical soil microorganisms.

L-lysine decarboxylase (LDC, EC 4.1.1.18) is a key enzyme in the decarboxylation of L-lysine to 1,5-pentanediamine and efficiently contributes significance to biosynthetic capability. Metagenomic technology is a shortcut approach used to obtain new genes from uncultured microorganisms. In this study, a subtropical soil metagenomic library was constructed, and a putative LDC gene named ldc1E was isolated by function-based screening strategy through the indication of pH change by L-lysine decarboxylation. Amino acid sequence comparison and homology modeling indicated the close relation between Ldc1E and other putative LDCs. Multiple sequence alignment analysis revealed that Ldc1E contained a highly conserved motif Ser-X-His-Lys (Pxl), and molecular docking results showed that this motif was located in the active site and could combine with the cofactor pyridoxal 5'-phosphate. The ldc1E gene was subcloned into the pET-30a(+) vector and highly expressed in Escherichia coli BL21 (DE3) pLysS. The recombinant protein was purified to homogeneity. The maximum activity of Ldc1E occurred at pH 6.5 and 40°C using L-lysine monohydrochloride as the substrate. Recombinant Ldc1E had apparent Km, kcat, and kcat/Km values of 1.08±0.16 mM, 5.09±0.63 s-1, and 4.73×103 s-1 M-1, respectively. The specific activity of Ldc1E was 1.53±0.06 U mg-1 protein. Identifying a metagenome-derived LDC gene provided a rational reference for further gene modifications in industrial applications.

Isolation and characterization of a gene associated with sulfate assimilation in Sinorhizobium fredii WGF03.

Sulfur is an essential element for rhizobia, such as sulfated modified Nod factors and nitrogenase. To investigate the role of sulfur metabolism in Rhizobium-Soybean symbiosis, a transponson random insertional mutants' library was constructed and a sulfur assimilation-related gene was isolated and characterized. A mutant strain unable to utilized sulfate was screened from 11,000 random insertional mutants of Sinorhizobium fredii WGF03. Sequencing analysis showed that a sulfate assimilation-related gene (cysDN) was inserted by the Tn transponson. Mutants inactivated in cysD and cysN (SMcysDF and SMcysNF) were constructed by homologous recombination using the suicide plasmid pK18mob. The mutants SMcysDF and SMcysNF could no longer utilize sulfate as sulfur source. Phenotype analysis revealed that mutation of cysDN had multiple effects on S. fredii WGF03. Root hair deformation assay showed that the activity of Nod factors secreted by mutants SMcysDR and SMcysNR elicited minimal hair initiation only. Soybean plant tests indicated that the mutant strains delayed 1-2 days to nodulate and exhibited lower nodulation efficiency and symbiotic efficiency than the wild-type strain. The complementary strain of cysD and cysN (HcysDF and HcysNF) could restore the nodulation efficiency.