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Bio-organic fertilizers (BOF) containing both organic amendments and beneficial microorganisms have been consistently shown to improve soils fertility and yield. However, the exact mechanisms which link amendments and yields remain disputed, and the complexity of bio-organic fertilizers may work in parallel in several ways. BOF may directly improve yield by replenishing soil nutrients or introducing beneficial microbial genes or indirectly by altering the soil microbiome to enrich native beneficial microorganisms. In this work, we aim to disentangle the relative contributions of direct and indirect effects on pear yield. We treated pear trees with either chemical fertilizer or organic fertilizer with/without the plant-beneficial bacterium Bacillus velezensis SQR9. We then assessed, in detail, soil physicochemical and biological properties (metagenome sequencing) as well as pear yield. We then evaluated the relative importance of direct and indirect effects of soil amendments on pear yield. Both organic treatments increased plant yield by up to 20%, with the addition of bacteria tripling the increase driven by organic fertilizer alone. This increase could be linked to alterations in soil physicochemical properties, bacterial community function, and metabolism. Supplementation of organic fertilizer SQR9 increased rhizosphere microbiome richness and functional diversity. Fertilizer-sensitive microbes and functions responded as whole guilds. Pear yield was most positively associated with the

Seagrass meadows are one of the most important marine ecosystems. Alkanes are the common hydrocarbon contaminants that can affect seagrass growth. In this study, a large spatial-scale investigation has been carried out on the alkane-degrading bacterial community structure in the rhizosphere and non-rhizosphere sediments of two seagrass species (Thalassia hemprichii and Halophila ovalis). AlkB gene was employed as a biomarker gene to study the alkane-degrading bacterial community structure. The results showed that the alpha diversity of the alkane-degrading bacterial community in T. hemprichii non-rhizosphere sediments was higher than that of its rhizosphere sediments. However, the alpha diversity of the alkane-degrading bacterial community in H. ovalis rhizosphere sediments was higher than that of its non-rhizosphere sediments in the open sea, but the result was contrast in the coast area. In addition, the alpha diversity of alkane-degrading bacterial communities in the coast area was higher than that of far away from the coast in the T. hemprichii rhizosphere and non-rhizosphere sediments. The phylogenetic analysis result revealed that the alkB sequences from the seagrass ecosystem were mainly affiliated with the class Alphaproteobacteria, and had the two novel lineages. Genus Agrobacterium was the most predominant alkane-degrading bacteria. These results contributed to disclose the geographical distribution pattern of alkane-degrading bacteria in the seagrass ecosystem of the South China Sea.

Seagrass meadows have seriously deteriorated in recent years. Seagrass associated phytate-mineralizing rhizobacteria potentially have functions related to seagrass nutrition, health and sustainable growth. The β-propeller phytases (BPPs) are the only phytase family in aquatic environments, but there are few studies on the BPP community structure of seagrass. In this study, clone libraries and quantitative PCR (qPCR) assays were used to compare the diversity and abundances of the BPP communities of Halodule endl, Halophila ovalis and Thalassia hemprichii in Xisha and Sanya, and to investigate the distribution characteristics of BPP genes in the rhizosphere sediment, which provedes insight into species specialty from phytic mineralization in subtropical and tropical seagrass ecosystems. The highest diversity of BPP genes was found for Thalassia hemprichii in Sanya Bay. Thalassia hemprichii in Sanya had higher abundances of BPPs, which were linked to Gammaproteobacteria. The BPP community diversity and OTUs of Thalassia hemprichii in Sanya were much higher than those of Thalassia hemprichii on Yongxing Island and Stone Island. The seagrass BPP communities had higher diversity and evenness from sampling sites with more human activity. The qPCR results showed that the abundance of phytate acid-degradating bacteria was approximately three times larger in Thalassia hemprichii rhizosphere sediment samples than in Halodule endl and Halophila ovalis rhizosphere sediment samples. This study highlighted that the diversity and abundances of bacteria genetically encoding BPP in the rhizosphere of Thalassia hemprichii were clearly higher than those of Halodule endl and Halophila ovalis. Further study of microbial phosphorus cycling will provide new insights into seagrass meadow ecosystems.

Coral reef ecosystems usually distribute in oligotrophic tropical and subtropical marine environments, but they possess great biodiversity and high productivity. It may attribute to its efficient internal nutrient cycle system. However, the knowledge of functional microbial community structure is still limited. In this study, both functional gene array (Geochip 5.0) and nifH Illumina sequencing were used to profile the overall functional genes and diazotrophic communities associated with coral Porites pukoensis. More than 7500 microbial functional genes were detected from archaea, bacteria, and fungi. Most of these genes are related to the transformation of carbon, nitrogen, sulfur, and phosphorus, providing evidence that microbes in the coral holobiont play important roles in the biogeochemical cycle of coral reef ecosystems. Our results indicated a high diversity of diazotrophs associated with corals. The dominant diazotrophic groups were related to phyla Alphaproteobacteria, Deltaproteobacteria, Cyanobacteria, and Gammaproteobacteria. And the dominant diazotrophic communities were divided into four clusters. They were affiliated with nifH sequences from genera Zymomonas, Halorhodospira, Leptolyngbya, Trichormus, and Desulfovibrio, indicating these groups may play a more important role in the nitrogen-fixing process in the coral holobiont. This study revealed functional gene diversity and suggested the roles they played in the biogeochemical cycling of the coral holobiont.

The community structure of coral associated microorganisms will change greatly in coral bleaching. However, the relationship between specific bacteria groups and Symbiodinium, which is easy to be found in the bleaching process, has been ignored for a long time. In this study, the changes of coral microbial community during a natural bleaching event in the South China Sea were studied by 16S rRNA gene high-throughput sequencing. The microbial community composition of bleached corals was significantly different from that of normal corals (P

The coral microbiome is one of the most complex microbial biospheres. However, the ecological processes shaping coral microbiome community assembly are not well understood. Here, we investigated the abundance, diversity, and community assembly mechanisms of coral-associated microbes from a highly diverse coral metacommunity in the South China Sea. Compared to seawater, the coral microbial metacommunity were defined by highly variable bacterial abundances among individual coral samples, high species evenness but not high species richness, high β-diversity, and a small core microbiome. We used variation partitioning analysis, neutral community model, and null model to disentangle the influences of different ecological processes in coral microbiome assembly. Measured physico-chemical parameters of the surrounding seawater and the spatial factor together explained very little of the variation in coral microbiome composition. Neutral processes only explained a minor component of the variation of coral microbial communities, suggesting a non-stochastic community assembly. Homogeneous and heterogeneous selection, but not dispersal, contributed greatly to the assembly of the coral microbiome. Such selection could be attributed to the within-host environments rather than the local environments. Our results demonstrated that dispersal limitation and host filtering contribute significantly to the assembly of discrete coral microbial regimes and expand the metacommunity diversity.

Seagrass ecosystems are among the most productive marine ecosystems, and diazotrophic communities play a crucial role in sustaining the productivity and stability of such ecosystems by introducing fixed nitrogen. However, information concerning both total and active diazotrophic groups existing in different compartments of seagrass is lacking. This study comprehensively investigated the diversity, structure, and abundance of diazotrophic communities in different parts of the seagrass Halophila ovalis at the DNA and RNA level from clone libraries and real-time quantitative PCR. Our results indicated that nearly one-third of existing nitrogen-fixing bacteria were active, and their abundance might be controlled by nitrogen to phosphorus ratio (N:P). Deltaproteobacteria and Gammaproteobacteria were dominant groups among the total and active diazotrophic communities in all samples. These two groups accounted for 82.21% and 70.96% at the DNA and RNA levels, respectively. The genus Pseudomonas and sulfate-reducing bacteria (genera: Desulfosarcina, Desulfobulbus, Desulfocapsa, and Desulfopila) constituted the significant fraction of nitrogen-fixing bacteria in the seagrass ecosystem, playing an additional role in denitrification and sulfate reduction, respectively. Moreover, the abundance of the nitrogenase gene, nifH, was highest in seawater and lowest in rhizosphere sediments from all samples. This study highlighted the role of diazotropic communities in the subtropical seagrass ecosystem.

Seagrasses constitute a significant part of coral reef ecosystems, representing high primary productivity and one of the most important coastal habitats in marine ecosystems. Though seagrasses possess irreplaceable ecological services to the marine environment, taxonomical ambiguity still exists due to similar morphological characters and phenotypic plasticity. As an emerging technology, DNA barcoding can effectively identify cryptic species using a short orthologous DNA region. In this study, we collected samples from five different locations (Daya Bay, Xincun Bay, Sanya Bay, Xisha Islands, and Nansha Islands), and three seagrass species Cymodocea rotundata, Thalassia hemprichii and Halophila ovalis was evaluated. Moreover, ITS, matK and rbcL genes were used as DNA barcodes. The results indicated that single ITS and concatenated ITS/matK/rbcL both conducted better species resolution than single matK and rbcL. Nevertheless, single ITS was more convenient. Furthermore, in all the four topology trees, three species resolved as 3 clusters as well H. ovalis and T. hemprichii grouped as sister clade. In the meantime, differentiation lay in intra-species based on the result of single ITS and three-locus analysis. Within H. ovalis and T. hemprichii separately, individuals from Xisha Islands first group together, then grouped with individuals from Nansha Islands and/or Xincun Bay and/or Sanya Bay and/or Daya Bay, which indicated that geographical distribution influenced population evolution. However, intra-species differentiation did not emerge in the tree of matK or rbcL.

The hypothesis of niche differentiation with respect to resources is considered to be one of the most influential explanations for the maintenance of species diversity. The hypothesis has been examined extensively by testing its prediction of species-habitat association, which posits that the spatial distribution of species is highly correlated with environmental variables. However, we argue that widespread evidence of the species-habitat association lacks adequate rigor to justify the niche differentiation hypothesis. In this study, we tested whether and to what extent the observed species-habitat association could be caused by ecological processes other than niche differentiation, in a 20-ha subtropical forest plot. The niche differentiation hypothesis was evaluated by testing the species-habitat association and performing a cross-evaluation of the habitat-diversity expectation, which posits that a strong positive correlation exists between species diversity and habitat complexity. Failure to support the habitat-diversity expectation would at a minimum indicate that the niche differentiation hypothesis might not be the main underlying process of species distribution, despite prevalence of the species-habitat association in the same plot. Our analysis revealed that distributions of most species (86.11%) in the plot were significantly associated with at least one of eight topographical and soil nutrient variables. However, there was almost no significant positive correlation between species diversity and habitat complexity at various spatial scales in the same plot. The results indicate that additional caution is warranted when interpreting the species-habitat association from the niche differentiation perspective. A significant species-habitat association indicates only a species’ habitat preference. The association may reveal nothing about interspecific differences in habitat preference, which is a requirement of the niche differentiation hypothesis.

Forest ecosystem productivity is crucial for regulating global climate change and carbon budget. Previous studies have shown that community diversity (such as species, functional and structural diversity) promotes forest productivity. However, species, functional, and structural diversity are often affected by canopy gap disturbance. In the context of global change, increases in canopy gap disturbance can augment the uncertainty in these relationships. Here, we used forest inventory, functional traits, and environmental data from a 20-ha subtropical forest plot located in the Zhejiang Province of China. We applied spatial synchronous autoregressive error modeling and structural equation models (SEMs) to analyze the effects of environmental factors (topography and soil properties), canopy gap disturbance (with and without the inclusion of the effect), community diversity variables on productivity. Results showed that stand structural diversity explained the largest amount of variation in productivity, followed by initial above-ground biomass and stand density. For canopy disturbed quadrats, stand structural explained the largest amount of variation in productivity, followed by stand density and species richness. For canopy non-disturbed quadrats, initial above-ground biomass explained the largest amount of variation in productivity, followed by stand density and stand structural diversity. Canopy gap disturbance enhanced the effect of stand structural diversity on productivity and reduced the effect of initial above-ground biomass. Our results provide strong evidence for the effect of canopy gap disturbance on the relationship between biodiversity and productivity in a subtropical forest. We argue that canopy gap disturbance reduces competition and promotes complementary utilization of resources, thus enhancing the impact of niche complementarity on productivity through species richness, stand density, and tree DBH diversity in forests.

Questions Mosaics of evergreen and deciduous trees that are characteristic of evergreen broad-leaved forests (EBLF) are thought to arise from habitat heterogeneity, but empirical evidence for this is limited. We test this assertion asking: (1) whether environmental heterogeneity explains the distribution of deciduous and evergreen trees; (2) which are the most important environmental variables; and (3) does their importance change with scale? Location Tiantong National Forest Park, Ningbo, Zhejiang, China. Methods We used data from a 20-ha individual-mapped EBLF in spatial point-pattern analyses testing the scale of aggregation within, and segregation between, the two life forms. We used a heterogeneous Poisson process model to remove the effects of environmental heterogeneity, predicting segregation would disappear if the mosaic was due to habitat heterogeneity alone. Finally, we tested the relative importance of theoretically important environmental variables using multivariate regression trees at three spatial scales (10, 20 and 50 m grid cells). Results We found evergreen and deciduous trees were aggregated at scales below 125 m and 60 m, respectively, and mutually exclusive at scales 0.27–0.30 g·kg−1 favouring deciduous species. Conclusions Our study is consistent with habitat heterogeneity creating the observed mosaics of evergreen and deciduous tree species, but micro-habitat heterogeneity contributed even at scales

Soil microbes re-establish plant diversity and ecosystem functions after disturbance events. Deterministic and stochastic processes are expected to contribute to microbial community assembly during long-term ecosystem recovery. We characterized soil prokaryotic and fungal communities, to determine their assembly patterns, along two chronosequences with early to later successional subtropical forests. Prokaryotic and fungal community composition was more variable in early successional forests but converged in the later successional forests. The community composition was governed by deterministic processes in the early stages, while the relative influence of stochasticity increased in the later stages. Environmental factors that predicted the shift in deterministic and stochastic balance varied within and across successional stages. In particular, the compositional dissimilarity of plant communities strongly predicted the relative influences of the two processes during succession. These findings suggest that the relative influences of deterministic and stochastic processes in shaping microbial community assembly shift during secondary succession. Consequently, plant communities are important predictors of assembly processes in soil microbial communities during long-term ecosystem recovery.

The responses of foliar nitrogen (N) and phosphorus (P) stoichiometry to nutrient additions are important indicators of various ecological processes, especially under climate change. However, how nutrient additions affect foliar N and P stoichiometry from species to community levels remain unclear, especially in P-limited systems. In this study, we conducted a nutrient additions experiment with control, N addition, P addition, and NP addition treatments in a P-limited subtropical forest to examine the effects of nutrient additions on foliar N and P stoichiometry. Our results showed that nutrient additions did not significantly influence foliar N concentration in seven dominant plant species over a three-year experimental period but significantly increased foliar P concentration and decreased foliar N:P ratio in species with lower initial foliar P concentration. The interactive effects of N and P additions on foliar P concentration and N:P ratio were synergistic and antagonistic, respectively. The response ratio of foliar P concentration to nutrient addition had a significantly negative correlation with initial foliar P concentration (r = −0.644), but had a positive one with initial foliar N:P ratio (r = 0.619). These results suggest that the limiting P dominated the responses of foliar N and P stoichiometry to nutrient additions at species level. At the community level, foliar P concentration and N:P ratio for both community weighted means (CWM) and community non-weighted means (CM) showed weaker positive responses to N and P additions than those at species level and there was no differential response between CWM and CM, suggesting the control of varied species responses on community foliar P concentration and N:P ratio response. Taken together, our results highlight the differential impacts of nutrient additions on foliar N and P stoichiometry between species and community levels, which needs to be considered in models when assessing the responses of ecosystem function to nutrient enrichments.

Co‐occurrence is a basic measure of spatial relationships between species. This commonly used measure has many benefits and limitations, yet a basic property that can strongly affect it has been overlooked. Co‐occurrence analysis is based on discrete sampling in space, and therefore, its grain size may affect the results and their interpretation, because species interactions and their environmental responses are scale‐dependent. We utilized a large dataset on tree species from a full‐stem mapped forest plot in China as a template for testing the effects of grain on species co‐occurrence patterns. We quantified co‐occurrence patterns for large trees and saplings in nested sampling plots with increasing radii and analyzed the effect of plot size on co‐occurrence. Co‐occurrence patterns varied greatly across grains. More than half of the species in large trees we analyzed had significantly non‐random co‐occurrence patterns at some grain. In contrast, saplings exhibited much fewer non‐random co‐occurrences. The proportion of segregated species pairs of large trees had a unimodal relationship with grain, whereas the proportion of aggregated species was positively related to grain. These patterns disappeared in saplings, suggesting that spatial interactions among trees are more prominent among larger individuals. Therefore, co‐occurrence patterns are scale‐dependent, and this scale dependency reflects a mixture of ecological (interspecific interactions, environmental responses) and statistical (sampling effects) processes. Our results suggest that insights from single‐grained studies cannot be generalized.

Seagrasses in coral reef ecosystems play important ecological roles by enhancing coral reef resilience under ocean acidification. However, seagrass primary productivity is typically constrained by limited nitrogen availability. Ammonia oxidation is an important process conducted by ammonia-oxidizing archaea (AOA) and bacteria (AOB), yet little information is available concerning the community structure and potential activity of seagrass AOA and AOB. Therefore, this study investigated the variations in the abundance, diversity and transcriptional activity of AOA and AOB at the DNA and transcript level from four sample types: the leaf, root, rhizosphere sediment and bulk sediment of seagrass Thalassia hemprichii in three coral reef ecosystems. DNA and complementary DNA (cDNA) were used to prepare clone libraries and DNA and cDNA quantitative PCR (qPCR) assays, targeting the ammonia monooxygenase-subunit (amoA) genes as biomarkers. Our results indicated that the closest relatives of the obtained archaeal and bacterial amoA gene sequences recovered from DNA and cDNA libraries mainly originated from the marine environment. Moreover, all the obtained AOB sequences belong to the Nitrosomonadales cluster. Nearly all the AOA communities exhibited higher diversity than the AOB communities at the DNA level, but the qPCR data demonstrated that the abundances of AOB communities were higher than that of AOA communities based on both DNA and RNA transcripts. Collectively, most of the samples shared greater community composition similarity with samples from the same location rather than sample type. Furthermore, the abundance of archaeal amoA gene in rhizosphere sediments showed significant relationships with the ammonium concentration of sediments and the nitrogen content of plant tissue (leaf and root) at the DNA level (P < 0.05). Conversely, no such relationships were found for the AOB communities. This work provides new insight into the nitrogen cycle, particularly nitrification of seagrass meadows in coral reef ecosystems.

Circular RNAs (circRNAs) play important roles in miRNA function and transcriptional control. However, little is known regarding circRNAs in the pear. In this study, we identified circRNAs using deep sequencing and analyzed their expression under drought stress. We identified 899 circRNAs in total, among which 33 (23 upregulated, 10 downregulated) were shown to be dehydration-responsive. We performed GO and KEGG enrichment analysis to predict the functions of differentially expressed circRNAs. 309 circRNAs were predicted to act as sponges for 180 miRNAs. A circRNA-miRNA co-expression network was constructed based on correlation analysis between the differentially expressed circRNAs and their miRNA binding sites. Our study will provide a rich genetic resource for the discovery of genes related to drought stress, and can readily be applied to other fruit trees.

© 2017 Zhang, Yang, Ling, Van Nostrand, Shi, Zhou and Dong. Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata, Avicennia marina, and Ceriops tagal, was undertaken using high-throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem.

Conspecific adults have strong negative effect on the survival of nearby early-stage seedlings and thus can promote species coexistence by providing space for the regeneration of heterospecifics. The leaf litter fall from the conspecific adults, and it could mediate this conspecific negative adult effect. However, field evidence for such effect of conspecific leaf litter remains absent. In this study, we used generalized linear mixed models to assess the effects of conspecific leaf litter on the early-stage seedling survival of four dominant species (Machilus leptophylla, Litsea elongate, Acer pubinerve and Distylium myricoides) in early-stage seedlings in a subtropical evergreen broad-leaved forest in eastern China. Our results consistently showed that the conspecific leaf litter of three species negatively affected the seedling survival. Meanwhile, the traditional conspecific adult neighborhood indices failed to detect this negative conspecific adult effect. Our study revealed that the accumulation of conspecific leaf litter around adults can largely reduce the survival rate of nearby seedlings. Ignoring it could result in underestimation of the importance of negative density dependence and negative species interactions in the natural forest communities.

The pervasive pattern of aggregated tree distributions in natural communities is commonly explained by the joint effect of two clustering processes: environmental filtering and dispersal limitation, yet little consensus remains on the relative importance of the two clustering processes on tree aggregations. Different life stages of examined species were thought to be one possible explanation of this disagreement, because the effect of environmental filtering and dispersal limitation are expected to increase and decrease with tree life stages, respectively. However, few studies have explicitly tested these expectations. In this study, we evaluated these expectations by three different methods (species-habitat association test based on Poisson Clustering model and spatial point pattern analyses based on Heterogeneous Poisson model and the jointly modeling approach) using 36 species in a 20-ha subtropical forest plot. Our results showed that the percentage of species with significant habitat association increased with life stages, and there were fewer species affected by dispersal limitation in later life stages compared with those in earlier stages. Percentage of variance explained by the environmental filtering and dispersal limitation also increases and decreases with life stages. These results provided a promising alternative explanation on the existing mixed results about the relative importance of the two clustering processes. These findings also highlighted the importance of plant life stages for fully understanding species distributions and species coexistence.

© 2016 Zhang, Yang, Ling, Van Nostrand, Shi, Zhou and Dong. The coral holobiont often resides in oligotrophic waters; both coral cells and their symbiotic dinoflagellates possess ammonium assimilation enzymes and potentially benefit from the nitrogen fixation of coral-associated diazotrophs. However, the seasonal dynamics of coral-associated diazotrophs are not well characterized. Here, the seasonal variations of diazotrophic communities associated with three corals, Galaxea astreata, Pavona decussata, and Porites lutea, were studied using nifH gene amplicon pyrosequencing techniques. Our results revealed a great diversity of coral-associated diazotrophs. nifH sequences related to Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria were ubiquitous and dominant in all corals in two seasons. In contrast with the coral P. decussata, both G. astreata and P. lutea showed significant seasonal changes in the diazotrophic communities and nifH gene abundance. Variable diazotroph groups accounted for a range from 11 to 49% within individual coral samples. Most of the variable diazotrophic groups from P. decussata were species-specific, however, the majority of overlapping variable groups in G. astreata and P. lutea showed the same seasonal variation characteristics. Rhodopseudomonas palustris- and Gluconacetobacter diazotrophicus-affiliated sequences were relatively abundant in the summer, whereas a nifH sequence related to Halorhodospira halophila was relatively abundant in spring G. astreata and P. lutea. The seasonal variations of all diazotrophic communities were significantly correlated with the seasonal shifts of ammonium and nitrate, suggesting that diazotrophs play an important role in the nitrogen cycle of the coral holobiont.

The phylogenetic diversity of coral-associated microbes has been extensively examined, but some contention remains regarding whether coral-associated microbial communities are species-specific or site-specific. It is suggested that corals may associate with microbes in terms of function, although little is known about the differences in coral-associated microbial functional gene composition and metabolic potential among coral species. Here, 16S rRNA Illumina sequencing and functional gene array (GeoChip 5.0) were used to assess coral-associated microbial communities. Our results indicate that both host species and environmental variables significantly correlate with shifts in the microbial community structure and functional potential. Functional genes related to key biogeochemical cycles including carbon, nitrogen, sulfur and phosphorus cycling, metal homeostasis, organic remediation, antibiotic resistance and secondary metabolism were shown to significantly vary between and among the four study corals (Galaxea astreata, Porites lutea, Porites andrewsi and Pavona decussata). Genes specific for anammox were also detected for the first time in the coral holobiont and positively correlated with ammonium. This study reveals that variability in the functional potential of coral-associated microbial communities is largely driven by changes in environmental factors and further demonstrates the importance of linking environmental parameters with genomic data in complex environmental systems.

Seagrass meadows represent one of the highest productive marine ecosystems and are of great ecological and economic values. Recently, they have been confronted with worldwide decline. Fungi play important roles in sustaining the ecosystem health as degraders of polycyclic aromatic hydrocarbons (PAHs), but fewer studies have been conducted in seagrass ecosystems. Hence, we investigated the dynamic variations of the fungal community succession under PAH stress in rhizosphere sediment of seagrasses Enhalus acoroides in this study. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), quantitative PCR (qPCR) and a clone library have been employed to analyze the fungal community’s shifts. Sequencing results of DGGE and the clone library showed that the predominant species belong to phyla Ascomycota and Basidiomycota. The abundance of three groups decreased sharply over the incubation period, whereas they demonstrated different fungal diversity patterns. Both the exposure time and the PAH concentrations affected the microbial diversity as assessed by PCR-DGGE analysis. Redundancy analysis (RDA) indicated that significant factors driving community shifts were ammonium and pH (p &lt, 0.05). Significant amounts of the variations (31.1%) were explained by pH and ammonium, illustrating that those two parameters were the most likely ones to influence or be influenced by the fungal communities’ changes. Investigation results also indicated that fungal communities in seagrass meadow were very sensitive to PAH-induced stress and may be used as potential indicators for the PAH contamination.

Coral associated bacterial community potentially has functions relating to coral health, nutrition and disease. Culture-free, 16S rRNA based techniques were used to compare the bacterial community of coral tissue, mucus and seawater around coral, and to investigate the relationship between the coral-associated bacterial communities and environmental variables. The diversity of coral associated bacterial communities was very high, and their composition different from seawater. Coral tissue and mucus had a coral associated bacterial community with higher abundances of Gammaproteobacteria. However, bacterial community in seawater had a higher abundance of Cyanobacteria. Different populations were also found in mucus and tissue from the same coral fragment, and the abundant bacterial species associated with coral tissue was very different from those found in coral mucus. The microbial diversity and OTUs of coral tissue were much higher than those of coral mucus. Bacterial communities of corals from more human activities site have higher diversity and evenness; and the structure of bacterial communities were significantly different from the corals collected from other sites. The composition of bacterial communities associated with same coral species varied with season’s changes, geographic differences, and coastal pollution. Unique bacterial groups found in the coral samples from more human activities location were significant positively correlated to chemical oxygen demand. These coral specific bacteria lead to coral disease or adjust to form new function structure for the adaption of different surrounding needs further research.