Revealing structure and assembly for rhizophyte-endophyte diazotrophic community in mangrove ecosystem after introduced Sonneratia apetala and Laguncularia racemosa

Exotic mangrove Laguncularia racemosa litter input accelerates nutrient cycling in mangrove ecosystems

Exotic plant litter presents different chemical and physical properties relative to native plant litter and alters ecosystem processes and functions that may facilitate exotic plant dispersal. However, these effects are largely unknown, especially within wetland ecosystems. This study examines whether introducing litter from the exotic mangrove Laguncularia racemosa could result in (1) accelerated community litter decomposition rates and increased nutrient cycling rates and (2) microbial community structure changes in the invaded areas. A single decomposition experiment using litterbags was conducted to examine the short-term effects of L. racemosa litter in the native mangrove forest ecosystem. The soil nutrients and microbial communities of Rhizophora stylosa, L. racemosa, and mixed forests were also compared to explore the long-term cumulative effects of L. racemosa litter in native ecosystems. The results indicated that L. racemosa has lower-quality leaf litter than R. stylosa and a significantly faster decomposition rate. This may result from changes in the soil microbial community structure caused by L. racemosa leaf litter input, which favors the decomposition of its own litter. Both the short-term and cumulative effect experiments demonstrated that L. racemosa leaf litter significantly increased the relative abundance of microbes related to litter decomposition, such as Proteobacteria and Bdellovibrionota, and enhanced the alpha diversity of soil fungi, thus creating a microbial environment conducive to L. racemosa leaf litter decomposition. Moreover, the accumulation of soil nutrients was lower under L. racemosa than under R. stylosa over several years. This may be related to the more rapid growth of L. racemosa, which causes soil nutrient absorption and storage within the plant tissues, thereby reducing the soil nutrient content. Inputting exotic mangrove L. racemosa leaf litter reduced the soil blue carbon content, potentially adversely affecting global climate change. L. racemosa may employ a unique strategy to lower soil nutrient levels in native mangroves based on its low-quality leaf litter, thereby weakening the competitive ability of native plants that are intolerant to low-nutrient conditions and enhancing its own competitive advantage to further spread into these areas. In summary, the input of exotic L. racemosa leaf litter accelerates nutrient cycling in local mangroves.

Species pool and soil properties in mangrove habitats influence the species-immigration process of diazotrophic communities across southern China

Microbial immigration is an ecological process in natural environments; however, the ecological trade-off mechanisms that govern the balance between species extinction and migration are still lacking. In this study, we investigated the mechanisms underlying the migration of diazotrophic communities from soil to leaves across six natural mangrove habitats in southern China. The results showed that the diazotrophic alpha and beta diversity exhibited significant regional and locational variations. The diazotrophic species pool gradually increased from the leaves to nonrhizosphere soil at each site, exhibiting a vertical distribution pattern. Mantel test analyses suggested that climate factors, particularly mean annual temperature, significantly influenced the structure of the diazotrophic community. The diazotrophic community assembly was mainly governed by dispersal limitation in soil and root samples, whereas dispersal limitation and ecological drift were dominant in leaves. Partial least squares path modeling revealed that the species pool and soil properties, particularly the oxidation-reduction potential and pH, were closely linked to the species-immigration ratio of diazotrophic communities. Our study provides novel insights for understanding the ecological trait diversity patterns and spread pathways of functional microbial communities between below- and aboveground habitats in natural ecosystems.IMPORTANCEEnvironmental selection plays key roles in microbial transmission. In this study, we have provided a comprehensive framework to elucidate the driving patterns of the ecological trade-offs in diazotrophic communities across large-scale mangrove habitats. Our research revealed that Bradyrhizobium japonicum, Marinobacterium lutimaris, and Agrobacterium tumefaciens were more abundant in root-associated soil than in leaves by internal and external pathways. The nonrhizospheric and rhizospheric soil samples harbored the most core amplicon sequence variants, indicating that these dominant diazotrophs could adapt to broader ecological niches. Correlation analysis indicated that the diversities of the diazotrophic community were regulated by biotic and abiotic factors. Furthermore, this study found a lower species immigration ratio in the soil than in the leaves. Both species pool and soil properties regulate the species-immigration mechanisms of the diazotrophic community. These results suggest that substantial species immigration is a widespread ecological process, leading to alterations in local community diversity across diverse host environments.

Methane and nitrous oxide emissions and related microbial communities from mangrove stems on Qi'ao Island, Pearl River Estuary in China

Mangrove forests, crucial carbon-rich ecosystems, are increasingly vulnerable to soil carbon loss and greenhouse gas (GHG) emissions due to human disturbance. However, the contribution of mangrove trees to GHG emissions remains poorly understood. This study monitored CO2, CH4, and N2O fluxes from the stems of two mangrove species, native Kandelia obovata (KO) and exotic Sonneratia apetala (SA), at three heights (0.7 m, 1.2 m, and 1.7 m) during the dry winter period on Qi'ao Island, Pearl River Estuary, China. Heartwood samples were analyzed to identify potential functional groups related to gas fluxes. Our study found that tree stems acted as both sinks and sources for N2O (ranging from -9.49 to 28.35 μg m-2 h-1 for KO and from -6.73 to 28.95 μg m-2 h-1 for SA) and CH4. SA exhibited significantly higher stem CH4 flux (from -26.67 to 97.33 μg m-2 h-1) compared to KO (from -44.13 to 88.0 μg m-2 h-1) (P < 0.05). When upscaled to the community level, both species were net emitters of CH4, contributing approximately 4.68 % (KO) and 0.51 % (SA) to total CH4 emissions. The decrease in stem CH4 flux with increasing height, indicates a soil source. Microbial analysis in the heartwood using the KEGG database indicated aceticlastic methanogenesis as the dominant CH4 pathway. The presence of methanogens, methanotrophs, denitrifiers, and nitrifiers suggests microbial involvement in CH4 and N2O production and consumption. Remarkably, the dominance of Cyanobacteria in the heartwood microbiome (with the relative abundance of 97.5 ± 0.6 % for KO and 99.1 ± 0.2 % for SA) implies roles in carbon and nitrogen fixation for mangroves coping with nitrogen limitation in coastal wetlands, and possibly in CH4 production. Although the present study has limitations in sampling duration and area, it highlights the significant role of tree stems in GHG emissions which is crucial for a holistic evaluation of the global carbon sequestration capability of mangrove ecosystems. Future research should broaden spatial and temporal scales to enhance the accuracy of upscaling tree stem gas fluxes to the mangrove ecosystem level.

Soil microbial community structure, function and network along a mangrove forest restoration chronosequence

Mangrove forests have high ecological, social and economic values, but due to environmental changes and human activities, natural mangrove forests have experienced serious degradations and reductions in distribution area worldwide. In the coastal zones of southern China, an introduced mangrove species, Sonneratia apetala, has been extensively used for mangrove restoration because of its rapid growth and strong environmental adaptability. However, little is known about how soil microorganisms vary with the restoration stages of the afforested mangrove forests. Here, we examined the changes in soil physicochemical properties and microbial biomass, community structure and function, and network in three afforested S. apetala forests with restoration time of 7, 12, and 18 years and compared them with a bare flat and a 60-year-old natural Kandelia obovata forest in a mangrove nature reserve. Our results showed that the contents of soil salinity, organic carbon, total nitrogen, ammonium nitrogen, and microbial biomass increased, while soil pH and bacterial alpha diversity decreased with afforestation age. Soil microbial community structure was significantly affected by soil salinity, organic carbon, pH, total nitrogen, ammonium nitrogen, available phosphorus, and available kalium, and susceptibility to environmental factors was more pronounced in bacterial than fungal community structure. The relative abundances of aerobic chemoheterotrophy were significantly higher in 12- and 18-year-old S. apetala than in K. obovata forest, while that of sulfate-reducing bacteria showed a decreasing trend with afforestation age. The abundance of dung saprotroph was significantly higher in 12- and 18-year-old S. apetala forests than in the natural forest. With the increasing afforestation age, the modularity of microbial networks increased, while stability and robustness decreased. Our results suggest that planting S. apetala contributes to improving soil fertility and microbial biomass but may make soil microbial networks more vulnerable.

Composition and assembly mechanisms of prokaryotic communities in wetlands, and their relationships with different vegetation and reclamation methods

Coastal wetlands are undergoing substantial transformations globally as a result of increased human activities. However, compared to other ecosystems, diversity and functional characteristics of microbial communities in reclaimed coastal wetlands are not well studied compared to other ecosystems. This is important because it is known that microorganisms can play a crucial role in biogeochemical cycling within coastal wetland ecosystems. Hence, this study utilized the high-throughput sequencing technique to investigate the structure and assembly processes of microbial communities in reclaimed coastal wetlands. The results revealed a substantial change in soil properties following coastal wetland reclamation. Remarkably, the reclaimed soil exhibited significantly lower pH, soil organic carbon (SOC), and total salinity (TS) values (p < 0.05). The dominant phyla included Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Planctomycetes among study sites. However, the relative abundance of Proteobacteria increased from un-reclaimed coastal wetlands to reclaimed ones. The Proteobacteria, Chloroflexi, and Acidobacteria showed higher relative abundance in vegetated soil compared to bare soil, while Bacteroidetes and Planctomycetes exhibited the opposite trend. Notably, vegetation types exerted the strongest influence on microbial diversity, surpassing the effects of soil types and depth (F = 34.49, p < 0.001; F = 25.49, p < 0.001; F = 3.173, p < 0.078, respectively). Stochastic assembly processes dominated in un-reclaimed soil, whereas deterministic processes governed the assembly in artificial sea embankment wetlands (SEW). The presence of Spartina alterniflora in all soil types (except SEW soils) indicated stochastic assembly, while Phragmites australis in reclaimed soils pointed toward deterministic microbial assembly. Furthermore, environmental factors such as pH, soil water content (SWC), SOC, total carbon (TC), total nitrogen (TN), total phosphorus (TP), NH4+-N, vegetation types, soil depth, and geographic distance exhibited significant effects on microbial beta diversity indices. Co-occurrence network analysis revealed a stronger association between taxa in SEW compared to land reclaimed from wetlands (LRW) and natural coastal wetlands (NCW). The bottom soil layer exhibited more complex network interactions than the topsoil layer. Besides soil parameters, reclamation and varieties of vegetation were also substantial factors influencing the composition, diversity, and assembly processes of microbial communities in coastal wetlands.

Diversity and structure of the root-associated bacterial microbiomes of four mangrove tree species, revealed by high-throughput sequencing

Background

Root-associated microbes of the mangrove trees play important roles in protecting and maintaining mangrove ecosystems. At present, most of our understanding of mangrove root-related microbial diversity is obtained from specific mangrove species in selected geographic regions. Relatively little is known about the composition of the bacterial microbiota existing in disparate mangrove species microenvironments, particularly the relationship among different mangrove species in tropical environments.

Methods

We collected the root, rhizosphere soil, and non-rhizosphere soil of four mangrove trees (Acanthus ilicifolius, Bruguiera gymnorrhiza, Clerodendrum inerme, and Lumnitzera racemosa) and detected the 16S rRNA gene by a conventional PCR. We performed high throughput sequencing using Illumina Novaseq 6000 platform (2 × 250 paired ends) to investigate the bacterial communities related with the different mangrove species.

Results

We analyzed the bacterial diversity and composition related to the diverse ecological niches of mangrove species. Our data confirmed distinct distribution patterns of bacterial communities in the three rhizocompartments of the four mangrove species. Microbiome composition varied with compartments and host mangrove species. The bacterial communities between the endosphere and the other two compartments were distinctly diverse independent of mangrove species. The large degree of overlap in critical community members of the same rhizocompartment across distinct mangrove species was found at the phylum level. Furthermore, this is the first report of Acidothermus found in mangrove environments. In conclusion, understanding the complicated host-microbe associations in different mangrove species could lay the foundation for the exploitation of the microbial resource and the production of secondary metabolites.

Environmental selection and evolutionary process jointly shape genomic and functional profiles of mangrove rhizosphere microbiomes

Mangrove reforestation with introduced species has been an important strategy to restore mangrove ecosystem functioning. However, how such activities affect microbially driven methane (CH4), nitrogen (N), and sulfur (S) cycling of rhizosphere microbiomes remains unclear. To understand the effect of environmental selection and the evolutionary process on microbially driven biogeochemical cycles in native and introduced mangrove rhizospheres, we analyzed key genomic and functional profiles of rhizosphere microbiomes from native and introduced mangrove species by metagenome sequencing technologies. Compared with the native mangrove (Kandelia obovata, KO), the introduced mangrove (Sonneratia apetala, SA) rhizosphere microbiome had significantly (p < 0.05) higher average genome size (AGS) (5.8 vs. 5.5 Mb), average 16S ribosomal RNA gene copy number (3.5 vs. 3.1), relative abundances of mobile genetic elements, and functional diversity in terms of the Shannon index (7.88 vs. 7.84) but lower functional potentials involved in CH4 cycling (e.g., mcrABCDG and pmoABC), N2 fixation (nifHDK), and inorganic S cycling (dsrAB, dsrC, dsrMKJOP, soxB, sqr, and fccAB). Similar results were also observed from the recovered Proteobacterial metagenome-assembled genomes with a higher AGS and distinct functions in the introduced mangrove rhizosphere. Additionally, salinity and ammonium were identified as the main environmental drivers of functional profiles of mangrove rhizosphere microbiomes through deterministic processes. This study advances our understanding of microbially mediated biogeochemical cycling of CH4, N, and S in the mangrove rhizosphere and provides novel insights into the influence of environmental selection and evolutionary processes on ecosystem functions, which has important implications for future mangrove reforestation.

Effects of waves, burial depth and material density on microplastic retention in coastal sediments

Coastal sediments, recognized as a major sink for microplastics (MPs), are subject to frequent physical disturbances, such as wave disturbance and associated sediment dynamics. Yet it remains poorly understood how wave disturbance regulates MPs accumulation in such a dynamic environment. Here, we examined the effects of waves and their interactions with material density and burial depth on the retention of MPs in coastal sediments, through manipulative experiments in a mangrove habitat along the coast of South China. The results clearly revealed that stronger waves removed more buried MPs from the sediments. Moreover, storms can have disproportional effects on MPs retention by inducing large waves and strong sediment erosion. We also demonstrated that MPs retention generally increased linearly with growing material density and non-linearly with raised burial depth in the sediment. Overall, our findings highlight the importance of both external and internal factors in shaping MPs retention in coastal ecosystems like mangroves, which is essential to assess and predict MPs accumulation patterns as well as its impacts on ecosystem functioning of such blue carbon habitats.

Assembly processes underlying bacterial community differentiation among geographically close mangrove forests

Bacterial communities play pivotal roles in nutrient cycling in mangrove forests. The assembly of mangrove microbial communities has been found to be influenced by complex factors, such as geographic distance, physicochemical conditions, and plant identity, but the relative importance of these factors and how these factors shape the assembling process remain elusive. We analyzed the bacterial communities sampled from three mangrove species (Aegiceras corniculatum, Bruguiera sexangula, and Kandelia obovata) at three locations along the estuarine Dongzhai Harbor in Hainan, China. We revealed larger differences in rhizosphere bacterial communities among geographical locations than among plant species, indicated by differences in diversity, composition, and interaction networks. We found that dispersal limitation and homogeneous selection have substantial contributions to the assembly of mangrove rhizosphere bacterial communities in all three locations. Following the phylogenetic-bin-based null model analysis (iCAMP) framework, we also found dispersal limitation and homogeneous selection showing dominance in some bins. The greater differences among geographic locations may be mainly attributed to the larger proportions of dispersal limitation even at such a short geographic distance. We also found that beta diversity was positively correlated with environmental distances, implying that the more similar environmental conditions (such as rich carbon and nitrogen contents) among plant species may have shaped similar bacterial communities. We concluded that the geographic distances, which are associated with dispersal limitation, played a key role in assembling mangrove rhizosphere bacterial communities, while physicochemical conditions and plant identity contributed less.

The role of bio-geomorphic feedbacks in shaping microplastic burial in blue carbon habitats

Coastal sediments are considered as hotspots of microplastics (MPs), with substantial MPs stocks found in blue carbon habitats such as mangroves and tidal marshes, where wave-damping vegetation reduces sediment erosion and enhances accretion. Here, we examined the effects of such bio-geomorphic feedbacks in shaping MPs burial, through a year-round field study in a mangrove habitat along the coast of South China. The results revealed that MPs abundance decreased significantly with the increase of cumulative sediment erosion as the strength of bio-geomorphic feedbacks declined. More shapes and colors of MPs were found at locations with weaker waves and less sediment erosion, where the average particle size was also higher. Our findings highlight the importance of bio-geomorphic feedbacks in affecting both the abundance and characteristics of the buried MPs. Such knowledge extends our understanding of MPs transport and burial from the perspective of bio-geomorphology, which is essential to assess and predict MPs accumulation patterns as well as its impacts on ecosystem functioning of the blue carbon habitats.

Ecological Processes of Bacterial and Fungal Communities Associated with Typha orientalis Roots in Wetlands Were Distinct during Plant Development

Root-associated microbiomes are essential for the ecological function of the root system. However, their assembly mechanisms in wetland are poorly understood. In this study, we explored and compared the ecological processes of bacterial and fungal communities in water, bulk soil, rhizosphere soil, and root endosphere niches for 3 developmental stages of Typha orientalis at different wetland sites, and assessed the potential functions of root endosphere microbiomes with function prediction. Our findings suggest that the microbial diversity, composition, and interaction networks along the water-soil-plant continuum are shaped predominantly by compartment niche and developmental stage, rather than by wetland site. Source tracking analysis indicated that T. orientalis' root endosphere is derived primarily from the rhizosphere soil (bacteria 39.9%, fungi 27.3%) and water (bacteria 18.9%, fungi 19.1%) niches. In addition, we found that the assembly of bacterial communities is driven primarily by deterministic processes and fungal communities by stochastic processes. The interaction network among microbes varies at different developmental stages of T. orientalis, and is accompanied by changes in microbial keystone taxa. The functional prediction data supports the distribution pattern of the bacterial and fungal microbiomes, which have different ecological roles at different plant developmental stages, where more beneficial bacterial taxa are observed in the root endosphere in the early stages, but more saprophytic fungi in the late stages. Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities and have significant implications for the future applications of plant microbiomes in the wetland ecosystem. IMPORTANCE Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities, and have significant implications for the future applications of plant microbiomes in the wetland ecosystem.

Temporal dynamics of total and active root-associated diazotrophic communities in field-grown rice

Plant-associated nitrogen-fixing microorganisms (diazotrophs) are essential to host nutrient acquisition, productivity and health, but how host growth affects the succession characteristics of crop diazotrophic communities is still poorly understood. Here, Illumina sequencing of DNA- and RNA-derived nifH genes was employed to investigate the dynamics of total and active diazotrophic communities across rhizosphere soil and rice roots under four fertilization regimes during three growth periods (tillering, heading and mature stages) of rice in 2015 and 2016. Our results indicated that 71.9–77.2% of the operational taxonomic units (OTUs) were both detected at the DNA and RNA levels. According to the nonmetric multidimensional scaling ordinations of Bray–Curtis distances, the variations in community composition of active rhizosphere diazotrophs were greater than those of total rhizosphere diazotrophs. The community composition (β-diversity) of total and active root-associated diazotrophs was shaped predominantly by microhabitat (niche; R² ≥ 0.959, p < 0.001), followed by growth period (R² ≥ 0.15, p < 0.001). The growth period had a stronger effect on endophytic diazotrophs than on rhizosphere diazotrophs. From the tillering stage to the heading stage, the α-diversity indices (Chao1, Shannon and phylogenetic diversity) and network topological parameters (edge numbers, average clustering coefficient and average degree values) of total endophytic diazotrophic communities increased. The proportions of OTUs shared by the total rhizosphere and endophytic diazotrophs in rhizosphere diazotrophs gradually increased during rice growth. Moreover, total diazotrophic α-diversity and network complexity decreased from rhizosphere soil to roots. Collectively, compared with total diazotrophic communities, active diazotrophic communities were better indicators of biological response to environmental changes. The host microhabitat profoundly drove the temporal dynamics of total and active root-associated diazotrophic communities, followed by the plant growth period.

Effects of single- and mixed-bacterial inoculation on the colonization and assembly of endophytic communities in plant roots

The introduction and inoculation of beneficial bacteria in plants have consistently been considered as one of the most important ways to improve plant health and production. However, the effects of bacterial inoculation on the community assembly and composition of the root endophytic microbiome remain largely unknown. In this study, 55 strains were randomly isolated from tomato roots and then inoculated into wheat seeds singly or in combination. Most of the isolated bacterial strains showed an ability to produce lignocellulose-decomposing enzymes and promote plant growth. The results demonstrated that bacterial inoculation had a significant effect on the wheat root endophytic microbiome. The wheat root samples inoculated with single-bacterial species were significantly separated into two groups (A and B) that had different community structures and compositions. Among these, root endophytic communities for most wheat samples inoculated with a single-bacterial strain (Group A) were predominated by one or several bacterial species, mainly belonging to Enterobacterales. In contrast, only a few of the root samples inoculated with a single-bacterial strain (Group B) harbored a rich bacterial flora with relatively high bacterial diversity. However, wheat roots inoculated with a mixed bacterial complex were colonized by a more diverse and abundant bacterial flora, which was mainly composed of Enterobacterales, Actinomycetales, Bacillales, Pseudomonadales, and Rhizobiales. The results demonstrated that inoculation with bacterial complexes could help plants establish more balanced and beneficial endophytic communities. In most cases, bacterial inoculation does not result in successful colonization by the target bacterium in wheat roots. However, bacterial inoculation consistently had a significant effect on the root microbiome in plants. CAP analysis demonstrated that the variation in wheat root endophytic communities was significantly related to the taxonomic status and lignocellulose decomposition ability of the inoculated bacterial strain (p < 0.05). To reveal the role of lignocellulose degradation in shaping the root endophytic microbiome in wheat, four bacterial strains with different colonization abilities were selected for further transcriptome sequencing analysis. The results showed that, compared with that in the dominant bacterial species Ent_181 and Ent_189 of Group A, the expression of lignocellulose-decomposing enzymes was significantly downregulated in Bac_133 and Bac_71 (p < 0.05). In addition, we found that the dominant bacterial species of the tomato endophytic microbiome were more likely to become dominant populations in the wheat root microbiome. In general, our results demonstrated that lignocellulose-decomposing enzymes played a vital role in the formation of endophytes and their successful colonization of root tissues. This finding establishes a theoretical foundation for the development of broad-spectrum probiotics.

Nitrite and nitrate reduction drive sediment microbial nitrogen cycling in a eutrophic lake

The anaerobic microbial nitrogen (N) removal in lake sediments is one of the most important processes driving the nitrogen cycling in lake ecosystems. However, the N removal and its underlying mechanisms regulated by denitrifying and anaerobic ammonia oxidation (anammox) bacteria in lake sediments remain poorly understood. With the field sediments collected from different areas of Lake Donghu (a shallow eutrophic lake), we examined the denitrifying and anammox bacterial communities by sequencing the nirS/K and hzsB genes, respectively. The results indicated that denitrifiers in sediments were affiliated to nine clusters, which are involved in both heterotrophic and autotrophic denitrification. However, anammox bacteria were only dominated by Candidatus Brocadia. We found that NO₃^- and NO₂^- concentrations, as well as Nar enzyme activity were the key factors affecting denitrifying and anammox communities in this eutrophic lake. The enrichment experiments in bioreactors confirmed the divergence of denitrification and anammox rates with an additional complement of NO₂^-, especially under a condition low nitrate reductase activity. The coupled denitrification and anammox may play significant roles in N removal, and the availability of electronic acceptors (i.e., NO₂^- and NO₃^-) strongly influenced the N loss in lake sediments. Further path analysis indicated that NO₂^-, NO₃^- and some N-related enzymes were the key factors affecting microbial N removal in lake sediments. This study advances our understanding of the mechanisms driving the of denitrification and anammox in lake sediments, which also provides new insights into coupled denitrification-anammox N removal in eutrophic lake ecosystems.

Metagenomic analysis of microbial communities continuously exposed to Bisphenol A in mangrove rhizosphere and non-rhizosphere soils

Bisphenol A (BPA) is widely distributed in littoral zones and may cause adverse impacts on mangrove ecosystem. Biodegradation and phytoremediation are two primary processes for BPA dissipation in mangrove soils. However, the rhizosphere effects of different mangrove species on BPA elimination are still unresolved. In this study, three typical mangrove seedlings, namely Avicennia marina, Bruguiera gymnorrhiza (L.) and Aegiceras corniculatum, were cultivated in soil microcosms for four months and then subjected to 28-day continuous BPA amendment. Un-planted soil microcosms (as control) were also set up. The BPA residual rates and root exudates were monitored, and the metabolic pathways as well as functional microbial communities were also investigated to decipher the rhizosphere effects based on metagenomic analysis. The BPA residual rates in all planted soils were significantly lower than that in un-planted soil on day 7. Both plantation and BPA dosage had significant effects on bacterial abundance. A distinct separation of microbial structure was found between planted and un-planted soil microcosms. Genera Pseudomonas and Lutibacter got enriched with BPA addition and may play important roles in BPA biodegradation. The shifts in bacterial community structure upon BPA addition were different among the microcosms with different mangrove species. Genus Novosphingobium increased in Avicennia marina and Bruguiera gymnorrhiza (L.) rhizosphere soils but decreased in Aegiceras corniculatum rhizosphere soil. Based on KEGG annotation and binning analysis, the proposal of BPA degradation pathways and the quantification of relevant functional genes were achieved. The roles of Pseudomonas and Novosphingobium may differ in lower BPA degradation pathways. The quantity variation patterns of functional genes during the 28-day BPA amendment were different among soil microcosms and bacterial genera.

Sugar and organic acid availability modulate soil diazotroph community assembly and species co-occurrence patterns on the Tibetan Plateau

Metabolites can mediate species interactions and the assembly of microbial communities. However, how these chemicals relate to the assembly processes and co-occurrence patterns of diazotrophic assemblages in root-associated soils remains largely unknown. Here, we examined the diversity and assembly of diazotrophic communities and further deciphered their links with metabolites on Tibetan Plateau. We found that the distribution of sugars and organic acids in the root-associated soils was significantly correlated with the richness of diazotrophs. The presence of these two soil metabolites explains the variability in diazotrophic community compositions. The differential concentrations of these metabolites were significantly linked with the distinctive abundances of diazotrophic taxa in same land types dominated by different plants or dissimilar soils by same plants. The assembly of diazotrophic communities is subject to deterministic ecological processes, which are widely modulated by the variety and amount of sugars and organic acids. Organic acids, for instance, 3-(4-hydroxyphenyl)propionic acid and citric acid, were effective predictors of the characteristics of diazotrophic assemblages across desert habitats. Diazotrophic co-occurrence networks tended to be more complex and connected within different land types covered by the same plant species. The concentrations of multiple sugars and organic acids were coupled significantly with the distribution of keystone species, such as Azotobacter, Azospirillum, Bradyrhizobium, and Mesorhizobium, in the co-occurrence network. These findings provide new insights into the assembly mechanisms of root-associated diazotrophic communities across the desert ecosystems of the Tibetan Plateau.Key points• Soil metabolites were significantly linked to the diversity of diazotrophic community.• Soil metabolites determined the assembly of diazotrophic community.• Sugars and organic acids were coupled mainly with keystone species in networks.

Nitrogen Fertilization and Native C4 Grass Species Alter Abundance, Activity, and Diversity of Soil Diazotrophic Communities

Native C4 grasses have become the preferred species for native perennial pastures and bioenergy production due to their high productivity under low soil nitrogen (N) status. One reason for their low N requirement is that C4 grasses may benefit from soil diazotrophs and promote biological N fixation. Our objective was to evaluate the impact of N fertilization rates (0, 67, and 202 kg N ha-1) and grass species (switchgrass [Panicum virgatum] and big bluestem [Andropogon gerardii]) on the abundance, activity, diversity, and community composition of soil diazotrophs over three agricultural seasons (grass green-up, initial harvest, and second harvest) in a field experiment in East Tennessee, United States. Nitrogen fertilization rate had a stronger influence on diazotroph population size and activity (determined by nifH gene and transcript abundances) and community composition (determined by nifH gene amplicon sequencing) than agricultural season or grass species. Excessive fertilization (202 kg N ha-1) resulted in fewer nifH transcripts compared to moderate fertilization (67 kg N ha-1) and decreased both richness and evenness of diazotrophic community, reflecting an inhibitory effect of high N application rates on soil diazotrophic community. Overall, cluster I and cluster III diazotrophs were dominant in this native C4 grass system. Diazotroph population size and activity were directly related to soil water content (SWC) based on structural equation modeling. Soil pH, SWC, and C and N availability were related to the variability of diazotrophic community composition. Our results revealed relationships between soil diazotrophic community and associated soil properties, adding to our understanding of the response of soil diazotrophs to N fertilization and grass species in native C4 grass systems.

Synergistic effects of antimony and arsenic contaminations on bacterial, archaeal and fungal communities in the rhizosphere of Miscanthus sinensis: Insights for nitrification and carbon mineralization

The impacts of metal(loids) on soil microbial communities are research focuses to understand nutrient cycling in heavy metal-contaminated environments. However, how antimony (Sb) and arsenic (As) contaminations synergistically affect microbially-driven ecological processes in the rhizosphere of plants is poorly understood. Here we examined the synergistic effects of Sb and As contaminations on bacterial, archaeal and fungal communities in the rhizosphere of a pioneer plant (Miscanthus sinensis) by focusing on soil carbon and nitrogen cycle. High contamination (HC) soils showed significantly lower levels of soil enzymatic activities, carbon mineralization and nitrification potential than low contamination (LC) environments. Multivariate analysis indicated that Sb and As fractions, pH and available phosphorus (AP) were the main factors affecting the structure and assembly of microbial communities, while Sb and As contaminations reduced the microbial alpha-diversity and interspecific interactions. Random forest analysis showed that microbial keystone taxa provided better predictions for soil carbon mineralization and nitrification under Sb and As contaminations. Partial least squares path modeling indicated that Sb and As contaminations could reduce the carbon mineralization and nitrification by influencing the microbial biomass, alpha-diversity and soil enzyme activities. This study enhances our understanding of microbial carbon and nitrogen cycling affected by Sb and As contaminations.

Microbially-driven sulfur cycling microbial communities in different mangrove sediments

Microbially-driven sulfur cycling is a vital biogeochemical process in the sulfur-rich mangrove ecosystem. It is critical to evaluate the potential impact of sulfur transformation in mangrove ecosystems. To reveal the diversity, composition, and structure of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) and underlying mechanisms, we analyzed the physicochemical properties and sediment microbial communities from an introduced mangrove species (Sonneratia apetala), a native mangrove species (Kandelia obovata) and the mudflat in Hanjiang River Estuary in Guangdong (23.27°N, 116.52°E), China. The results indicated that SOB was dominated by autotrophic Thiohalophilus and chemoautotrophy Chromatium in S. apetala and K. obovata, respectively, while Desulfatibacillum was the dominant genus of SRB in K. obovata sediments. Also, the redundancy analysis indicated that temperature, redox potential (ORP), and SO₄^2- were the significant factors influencing the sulfur cycling microbial communities with elemental sulfur (ES) as the key factor driver for SOB and total carbon (TC) for SRB in mangrove sediments. Additionally, the morphological transformation of ES, acid volatile sulfide (AVS) and SO₄^2- explained the variation of sulfur cycling microbial communities under sulfur-rich conditions, and we found mangrove species-specific dominant Thiohalobacter, Chromatium and Desulfatibacillum, which could well use ES and SO₄^2-, thus promoting the sulfur cycling in mangrove sediments. Meanwhile, the change of nutrient substances (TN, TC) explained why SOB were more susceptible to environmental changes than SRB. Sulfate reducing bacteria produces sulfide in anoxic sediments at depth that then migrate upward, toward fewer reducing conditions, where it's oxidized by sulfur oxidizing bacteria. This study indicates the high ability of SOB and SRB in ES, SO₄^2-_,S₂^- and S^2- generation and transformation in sulfur-rich mangrove ecosystems, and provides novel insights into sulfur cycling in other wetland ecosystems from a microbial perspective.

Patterns and drivers of microeukaryotic distribution along the North Equatorial Current from the Central Pacific Ocean to the South China Sea

Microeukaryotes have been recognized as highly abundant and diverse both in form and function, however, data on their diversity and distribution along marine currents remain scarce. Herein, the distribution of microeukaryotes in surface seawaters was analyzed along a 9000 km stretch of the North Equatorial Current (NEC) and its bifurcation using high throughput DNA sequencing. Significant distance-decay patterns were detected, and the microeukaryote communities were further divided into Central Pacific Ocean (CPO), Western Pacific Ocean (WPO), and South China Sea (SCS) groups. Statistical analyses suggested that the microeukaryotic assembly in the WPO is maintained by the CPO community transported via the NEC. Environmental selection contributed more to community variations than spatial processes did. Temperature and salinity were the two most important environmental factors to shape the examined communities. Altogether, characterizing the microeukaryotic diversity and distribution along the NEC provided an insight into the drivers of their distribution in open oceans.

Martelella alba sp. nov., isolated from mangrove rhizosphere soil within the Beibu Gulf

Strain BGMRC 2036^T was isolated from rhizosphere soil of Bruguiear gymnorrhiza collected from the Beibu Gulf of China. Optimum growth occurred at 28 °C, pH 7.0, and under the conditions of 3-5% (w/v) NaCl. The phylogenetic comparisons of 16S rRNA gene sequences displayed that strain BGMRC 2036^T was closely related to Martelella limonii NBRC109441^T (96.6% sequence similarity), M. mediterranea CGMCC 1.12224^T (96.5%), M. lutilitoris GH2-6^T (96.5%), M. radicis BM5-7^T (96.2%), and M. mangrove BM9-1^T (95.9%), M. suaedae NBRC109440^T (95.8%). The phylogenomic tree based on the up-to-date bacterial core gene set indicated that the strain BGMRC 2036^T form a clade formed with members of the genera Martelella. The major polar lipids include phosphatidylmethylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphotidylinositol, two unidentified phospholipids, and three unidentified ninhydrin positive phospholipids. The major respiratory quinone is Q-10, which is similar to those of genera Martelella. The main cellular fatty acids are C_18:1 ω7c, C_16:0, and C_12:0 aldehyde. Genome sequencing revealed a genome size of 4.99 Mbp and a G + C content of 62.3 mol%. Pairwise comparison of the genomes of the new strain BGMRC 2036^T and the three reference strains M. endophytica YC 6887^T, M. mediterranea CGMCC 1.12224^T, and M. mangrovi USBA-857 indicated that gANI value was lower than 81% and a digital DNA-DNA hybridization value was lower than 27%. The strain BGMRC 2036^T possessed genes putatively encoding riboflavin synthesis and flavodoxin A polyphasic taxonomic study suggested that strain BGMRC 2036^T represented a novel species belonging to the genus Martelella, and it was named Martelella alba sp. nov. The type strain is BGMRC 2036^T (=KCTC 52121^T =NBRC 111908^T).

Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale

Mangrove roots harbor a repertoire of microbial taxa that contribute to important ecological functions in mangrove ecosystems. However, the diversity, function, and assembly of mangrove root-associated microbial communities along a continuous fine-scale niche remain elusive. Here, we applied amplicon and metagenome sequencing to investigate the bacterial and fungal communities among four compartments (nonrhizosphere, rhizosphere, episphere, and endosphere) of mangrove roots. We found different distribution patterns for both bacterial and fungal communities in all four root compartments, which could be largely due to niche differentiation along the root compartments and exudation effects of mangrove roots. The functional pattern for bacterial and fungal communities was also divergent within the compartments. The endosphere harbored more genes involved in carbohydrate metabolism, lipid transport, and methane production, and fewer genes were found to be involved in sulfur reduction compared to other compartments. The dynamics of root-associated microbial communities revealed that 56-74% of endosphere bacterial taxa were derived from nonrhizosphere, whereas no fungal OTUs of nonrhizosphere were detected in the endosphere. This indicates that roots may play a more strictly selective role in the assembly of the fungal community compared to the endosphere bacterial community, which is consistent with the projections established in an amplification-selection model. This study reveals the divergence in the diversity and function of root-associated microbial communities along a continuous fine-scale niche, thereby highlighting a strictly selective role of soil-root interfaces in shaping the fungal community structure in the mangrove root systems.

Soil metabolome correlates with bacterial diversity and co-occurrence patterns in root-associated soils on the Tibetan Plateau

Metabolites in root-zone soils mediate microbe-to-microbe interactions and govern the overall microbial community. However, how chemicals relate to diversity and co-occurrence patterns of bacterial communities in root-associated soils is still poorly understood. Here, we studied the relationships of soil metabolome with bacterial community diversity and co-occurrence patterns in root-associated soils across different land types on the Tibetan Plateau. The soil metabolome mainly encompassed a range of organic acids, and sugars and sugar derivatives, which were widely negatively correlated with bacterial alpha-diversity. Compared to the investigated environmental variables, metabolites accounted more for the variations in the Shannon diversity and bacterial community compositions. Compared to sugars, organic acids accounted more for bacterial community compositions at high taxonomic ranks, while reversed at genus and species levels. The relative abundances of some bacterial genera and metabolites were closely linked to soil types and plant genotypes. The differential compounds were significantly correlated with the distinctive bacterial taxa across land types and plant genotypes. Keystone species in co-occurrence network, such as Bradyrhizobium, Bryobacter, and Microvirga were significantly correlated with sugars and organic acids. Structural equation modeling revealed that sugar metabolism can play a crucial role in altering the bacterial community diversity. This study provides new insights into the ecological mechanism that maintains bacterial community in the root-associated soils on the Tibetan Plateau.