Sulphur-oxidizing and sulphate-reducing communities in Brazilian mangrove sediments

Biogeochemical mechanisms of zero-valent iron and biochar for synergistically mitigating antimony uptake in rice

Antimony (Sb) contamination in paddy fields can lead to its accumulation in rice grains, posing a threat to food safety. To address this issue, the combined use of zero-valent iron (ZVI) and biochar (BC) were applied to decrease the uptake of Sb in Sb-polluted soils, and their effects on Sb uptake from soil to rice grains were investigated. Our results showed that the combination treatment of 0.05% ZVI and 0.095% BC resulted in a significant decrease (42.8%) in Sb accumulation in rice grains that was comparably more efficient than that by 0.05% ZVI (decrease of 15.8% Sb accumulation) or 0.095% BC (decrease of 12.7% Sb accumulation) alone, demonstrating the synergistic effect of ZVI and BC on mitigating Sb uptake by rice plants. ZVI presence resulted in the formation of iron oxides in the soil and on root surfaces, and the S2-/S22- ascent also increased by 58.7% on day 75 compared with that of the control, facilitating the reduction of Sb(V) to less mobile Sb(III), thereby decreasing Sb accumulation in rice plants. BC initially increased the mobility of Sb owing to its alkaline nature, whereas the electron shuttle properties of BC contributed to a decrease in Sb mobility. The abundance of the arsenite-reducing gene arrA ultimately increased by 203.2% on day 120 compared with the initial phase on day 5, and BC caused a remarkable increase in arrA gene abundance. This study revealed the synergistic mechanisms by combining ZVI and BC to mitigate Sb uptake by rice, which may be useful for the sustainable remediation of contaminated rice paddies.

Spatial characteristics of microbial communities and their functions in sediments of subtropical Beibu Gulf, China

Understanding the intricate relationship between marine geography and microbial functions is crucial for marine conservation and management. In this study, we conducted a comprehensive analysis of bacterial composition and function in nearshore and offshore sediments of the Beibu Gulf using 16S rRNA high-throughput sequencing. The results showed that Proteobacteria (average relative abundance: 27.07 %) and Desulfobacterota (average relative abundance: 12.28 %) were the most dominant phyla across all stations, while Woeseiaceae (3.26 %-8.31 %) and Anaerolineaceae (0.61 %-7.43 %) could serve as potential indicator species for pollution. In our study area, the α-diversity of bacterial communities in sediment samples showed an initial increase from coastal to offshore regions, followed by a decrease with further distance from the coastlines. The composition of sediment bacterial communities was mainly influenced by total phosphorus (R2 = 0.183, p < 0.01) and salinity (R2 = 0.550, p < 0.01). Furthermore, the sulfur (S) cycling genes of KEGG pathways displayed significant variations with the distance from shore, implying that S oxidation dominated in nearshore sediments, while S reduction occurred mainly in offshore sediments, which was attributed to the differences in redox conditions across diverse marine environments. These findings will not only enhance our current understanding of the intricate relationship between marine geography and microbial functions but also contribute to elucidating the biogeochemical characteristics of the Beibu Gulf. This research will provide valuable information and a solid scientific basis for the conservation and management of various marine areas.

Eco-resilience of China's mangrove wetlands: The impact of heavy metal pollution and dynamics

Mangrove forests in China have significantly degraded over the past several decades primarily due to rapid economic growth and land reclamation for aquaculture and infrastructure development. Among various threats, heavy metal pollution, primarily from urbanization, agricultural runoff, and industrial runoff, poses a substantial risk to mangroves in China. It impairs their ecological functions, limiting biodiversity and reducing their natural ability to sequester carbon and detoxify coastal areas. Despite these challenges, the mangrove ecosystem's resilience in China has not been completely compromised. Natural adaptations and phytoremediation mechanisms, such as limiting metal uptake, excreting metal binding proteins, upregulating antioxidants, forming Fe plague, excreting metals through salt glands, and tolerance to specific metal concentrations, help mitigate heavy metal toxicity. However, these adaptive strategies are limited by the extent of pollutants and the speed at which these pollution factors arise. This review highlights a need to shift restoration efforts from expanding mangrove areas to enhancing ecosystem integrity, with a specific focus on reducing heavy metal pollution through phytoremediation. It also examines how heavy metal interactions at the sediment-water interface impact microbial communities and local fauna, contributing to climate change. Addressing these challenges is critical to improving mangrove conservation in China and ensuring the long-term health and resilience of these critical ecosystems for future generations.

Microbial community dynamics and bioremediation strategies for petroleum contamination in an in-service oil Depot, middle-lower Yellow River Basin

This study investigated soil and groundwater contamination at an in-service oil transportation station in the middle-lower Yellow River Basin, China. Spatial analysis combined with 16S rRNA and ITS sequencing revealed localized heavy metal (Cu, Ni, Cd, Pb) and petroleum hydrocarbon (PHs: 15.0 mg/kg) contamination in the oily sewage treatment area, with vertical migration constrained by silty sand layers. Volatile organic compounds (VOCs) primarily originated from oil tank emissions. Groundwater exhibited hydraulic gradient-driven downstream migration of PHs (0.03-0.04 mg/L) and arsenic (1.1-1.5 μg/L). Indigenous microbial communities exhibited redox-stratified functional differentiation: unclassified Comamonadaceae (Proteobacteria) dominated aerobic zones (monitoring well D5), utilizing nitrate for PHs degradation, while Desulfosporosinus (Firmicutes) mediated sulfate-coupled anaerobic alkane degradation and metal immobilization in anoxic zones (D6). Fungal communities featured Trametes (Basidiomycota), facilitating ligninolytic PAH breakdown via peroxidase secretion. Functional prediction (FAPROTAX/FUNGuild) confirmed a synergistic "fungal preprocessing-bacterial mineralization" mechanism. Microbial metabolic plasticity (e.g., nitrogen respiration, photoautotrophy) enabled adaptation to redox fluctuations. Given the site's medium-low risk profile, we proposed a tiered management framework: (1) in situ bioremediation that prioritizes indigenous microbes, (2) hierarchical risk zoning, and (3) dynamic monitoring networks. These strategies align with China's Green Low-Carbon Remediation principles through low-energy microbial technologies. The findings provide a mechanistic basis for balancing industrial operations and ecological health in the Yellow River Basin.

Metagenomic surveillance reveals different structure and function of microbial community associated with mangrove pneumatophores and their surrounding matrices

Present research employed metagenomics to explore the structural and functional diversity of microorganisms in two matrices of pneumatophore: adhered sediments (PS) and epiphytes (PE) of Avicennia marina. These were compared with microorganisms in surrounding environments: tidal water (TW), mudflat sediment (MF) and mangrove sediment (MS). Results revealed that bacteria made up over 95 % of the microbial community across all five matrices, with the dominance of phylum Proteobacteria, because of their metabolic flexibility and ability to survive in harsh mangrove environment. The bacterial community in PS and PE were similar to TW but differed from those in MF and MS, implying their provenance from TW. The high relative abundance of genes involved in nitrate and sulfur reduction pathways in PS and PE indicates pneumatophore bacteria helps in enhancing nitrogen and sulfur availability. This study is the first to explore the functional significance of pneumatophore-adhered prokaryotic communities using metagenomics.

Organic matter decay and bacterial community succession in mangroves under simulated climate change scenarios

Mangroves are coastal environments that provide resources for adjacent ecosystems due to their high productivity, organic matter decomposition, and carbon cycling by microbial communities in sediments. Since the industrial revolution, the increase of Greenhouse Gases (GHG) released due to fossil fuel burning led to many environmental abnormalities such as an increase in average temperature and ocean acidification. Based on the hypothesis that climate change modifies the microbial diversity associated with decaying organic matter in mangrove sediments, this study aimed to evaluate the microbial diversity under simulated climate change conditions during the litter decomposition process and the emission of GHG. Thus, microcosms containing organic matter from the three main plant species found in mangroves throughout the State of São Paulo, Brazil (Rhizophora mangle, Laguncularia racemosa, and Avicennia schaueriana) were incubated simulating climate changes (increase in temperature and pH). The decay rate was higher in the first seven days of incubation, but the differences between the simulated treatments were minor. GHG fluxes were higher in the first ten days and higher in samples under increased temperature. The variation in time resulted in substantial impacts on α-diversity and community composition, initially with a greater abundance of Gammaproteobacteria for all plant species despite the climate conditions variations. The PCoA analysis reveals the chronological sequence in β-diversity, indicating the increase of Deltaproteobacteria at the end of the process. The GHG emission varied in function of the organic matter source with an increase due to the elevated temperature, concurrent with the rise in the Deltaproteobacteria population. Thus, these results indicate that under the expected climate change scenario for the end of the century, the decomposition rate and GHG emissions will be potentially higher, leading to a harmful feedback loop of GHG production. This process can happen independently of an impact on the bacterial community structure due to these changes.

Microbiome divergence of marine gastropod species separated by the Isthmus of Panama

The rise of the Isthmus of Panama separated the populations of many marine organisms, which then diverged into new geminate sister species currently living in the Eastern Pacific Ocean and the Caribbean Sea. However, we know very little about how such evolutionary divergences of host species have shaped the compositions of their microbiomes. Here, we compared the microbiomes of whole-body and shell-surface samples of geminate species of marine gastropods in the genera Cerithium and Cerithideopsis to those of congeneric outgroups. Our results suggest that the effects of ~3 million years of separation and isolation on microbiome composition varied among host genera and between sample types within the same hosts. In the whole-body samples, microbiome compositions of geminate species pairs tended to be similar, likely due to host filtering, although the strength of this relationship varied among the two groups and across similarity metrics. Shell-surface microbiomes show contrasting patterns, with co-divergence between the host taxa and a small number of microbial clades evident in Cerithideopsis but not Cerithium. These results suggest that (i) isolation of host populations after the rise of the Isthmus of Panama affected microbiomes of geminate hosts in a complex and host-specific manner, and (ii) host-associated microbial taxa respond differently to vicariance events than the hosts themselves.IMPORTANCEWhile considerable work has been done on evolutionary divergences of marine species in response to the rise of the Isthmus of Panama, which separated two previously connected oceans, how this event shaped the microbiomes of these marine hosts remains poorly known. Using whole-body and shell-surface microbiomes of closely related gastropod species from opposite sides of the Isthmus, we show that divergences of microbial taxa after the formation of the Isthmus are often not concordant with those of their gastropod hosts. Our results show that evolutionary responses of marine gastropod-associated microbiomes to major environmental perturbations are complex and are shaped more by local environments than host evolutionary history.

Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan

BACKGROUND

Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions.

RESULTS

The results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation.

CONCLUSION

Our findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community.

Living in mangroves: a syntrophic scenario unveiling a resourceful microbiome

BACKGROUND

Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availability, among other factors, drives the microbial community composition, favoring syntrophic populations harboring a rich and diverse, stress-driven metabolism. Mangroves are known for their carbon sequestration capability, and their complex and integrated metabolic activity is essential to global biogeochemical cycling. Here, we present a metabolic reconstruction based on the genomic functional capability and flux profile between sympatric MAGs co-assembled from a tropical restored mangrove.

RESULTS

Eleven MAGs were assigned to six Bacteria phyla, all distantly related to the available reference genomes. The metabolic reconstruction showed several potential coupling points and shortcuts between complementary routes and predicted syntrophic interactions. Two metabolic scenarios were drawn: a heterotrophic scenario with plenty of carbon sources and an autotrophic scenario with limited carbon sources or under inhibitory conditions. The sulfur cycle was dominant over methane and the major pathways identified were acetate oxidation coupled to sulfate reduction, heterotrophic acetogenesis coupled to carbohydrate catabolism, ethanol production and carbon fixation. Interestingly, several gene sets and metabolic routes similar to those described for wastewater and organic effluent treatment processes were identified.

CONCLUSION

The mangrove microbial community metabolic reconstruction reflected the flexibility required to survive in fluctuating environments as the microhabitats created by the tidal regime in mangrove sediments. The metabolic components related to wastewater and organic effluent treatment processes identified strongly suggest that mangrove microbial communities could represent a resourceful microbial model for biotechnological applications that occur naturally in the environment.

Response of microbial diversity and function to the degradation of Barkol Saline Lake

Barkol Lake, a shrinking hypersaline lake situated in the northeast of Xinjiang, China, has experienced the exposure of its riverbed and the gradual drying up of its original sediment due to climate change and human activities, resulting in the formation of alkaline soils. These changes have correspondingly altered the physicochemical characteristics of the surrounding environment. Microorganisms play a crucial role, with special functioning involved in various nutrient cycling and energy transfer in saline lake environments. However, little is known about how the microbial community dynamics and metabolic functions in this shrinking saline lake relate to the degradation process. To address this knowledge gap, a cultivation-independent method of amplicon sequencing was used to identify and analyze the microbial community and its potential ecological functions in the sediment and degraded area. The microbial community diversity was found to be significantly lower in the degraded areas than in the sediment samples. The Pseudomonadota was dominant in Barkol Saline Lake. The abundance of Desulfobacterota and Bacillota in the degraded areas was lower than in the lake sediment, while Pseudomonadota, Acidobacteriota, and Actinobacteriota showed an opposite trend. The βNTI showed that microbial community assembly was primarily associated with deterministic processes in Barkol Saline Lake ecosystems and stochastic processes at the boundary between sediment and degraded areas. Functional predictions showed that sulfur metabolism, particularly sulfate respiration, was much higher in sediment samples than in the degraded areas. Overall, these findings provided a possible perspective for us to understand how microorganisms adapt to extreme environments and their role in saline lakes under environmental change.

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.

The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival

BACKGROUND

Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and if not for microbial cycling of nutrients, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse on the planet, and serve vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and sequester carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome in Southeast Asia are scarce.cxs RESULTS: Here we examine the microbiome of Avicenia alba and Sonneratia alba and identify a core microbiome of 81 taxa. A further eight taxa (Pleurocapsa, Tunicatimonas, Halomonas, Marinomonas, Rubrivirga, Altererythrobacte, Lewinella, and Erythrobacter) were found to be significantly enriched in mangrove tree compartments suggesting key roles in this microbiome. The majority of those identified are involved in nutrient cycling or have roles in the production of compounds that promote host survival.

CONCLUSION

The identification of a core microbiome furthers our understanding of mangrove microbial biodiversity, particularly in Southeast Asia where studies such as this are rare. The identification of significantly different microbial communities between sampling sites suggests environmental filtering is occurring, with hosts selecting for a microbial consortia most suitable for survival in their immediate environment. As climate change advances, many of these microbial communities are predicted to change, however, without knowing what is currently there, it is impossible to determine the magnitude of any deviations. This work provides an important baseline against which change in microbial community can be measured.

The microbial landscape in bioturbated mangrove sediment: A resource for promoting nature-based solutions for mangroves

Globally, soils and sediments are affected by the bioturbation activities of benthic species. The consequences of these activities are particularly impactful in intertidal sediment, which is generally anoxic and nutrient-poor. Mangrove intertidal sediments are of particular interest because, as the most productive forests and one of the most important stores of blue carbon, they provide global-scale ecosystem services. The mangrove sediment microbiome is fundamental for ecosystem functioning, influencing the efficiency of nutrient cycling and the abundance and distribution of key biological elements. Redox reactions in bioturbated sediment can be extremely complex, with one reaction creating a cascade effect on the succession of respiration pathways. This facilitates the overlap of different respiratory metabolisms important in the element cycles of the mangrove sediment, including carbon, nitrogen, sulphur and iron cycles, among others. Considering that all ecological functions and services provided by mangrove environments involve microorganisms, this work reviews the microbial roles in nutrient cycling in relation to bioturbation by animals and plants, the main mangrove ecosystem engineers. We highlight the diversity of bioturbating organisms and explore the diversity, dynamics and functions of the sediment microbiome, considering both the impacts of bioturbation. Finally, we review the growing evidence that bioturbation, through altering the sediment microbiome and environment, determining a 'halo effect', can ameliorate conditions for plant growth, highlighting the potential of the mangrove microbiome as a nature-based solution to sustain mangrove development and support the role of this ecosystem to deliver essential ecological services.

Stable Isotopic and Metagenomic Analyses Reveal Microbial-Mediated Effects of Microplastics on Sulfur Cycling in Coastal Sediments

Microplastics are readily accumulated in coastal sediments, where active sulfur (S) cycling takes place. However, the effects of microplastics on S cycling in coastal sediments and their underlying mechanisms remain poorly understood. In this study, the transformation patterns of different S species in mangrove sediments amended with different microplastics and their associated microbial communities were investigated using stable isotopic analysis and metagenomic sequencing. Biodegradable poly(lactic acid) (PLA) microplastics treatment increased sulfate (SO₄^2-) reduction to yield more acid-volatile S and elementary S, which were subsequently transformed to chromium-reducible S (CRS). The S isotope fractionation between SO₄^2- and CRS in PLA treatment increased by 9.1‰ from days 0 to 20, which was greater than 6.8‰ in the control. In contrast, recalcitrant petroleum-based poly(ethylene terephthalate) (PET) and polyvinyl chloride (PVC) microplastics had less impact on the sulfate reduction, resulting in 7.6 and 7.7‰ of S isotope fractionation between SO₄^2- and CRS from days 0 to 20, respectively. The pronounced S isotope fractionation in PLA treatment was associated with increased relative abundance of Desulfovibrio-related sulfate-reducing bacteria, which contributed a large proportion of the microbial genes responsible for dissimilatory sulfate reduction. Overall, these findings provide insights into the potential impacts of microplastics exposure on the biogeochemical S cycle in coastal sediments.

Contrasting archaeal and bacterial community assembly processes and the importance of rare taxa along a depth gradient in shallow coastal sediments

Marine microbial communities assemble along a sediment depth gradient and are responsible for processing organic matter. Composition of the microbial community along the depth is affected by various biotic and abiotic factors, e.g., the change of redox gradient, the availability of organic matter, and the interactions of different taxa. The community structure is also subjected to some random changes caused by stochastic processes of birth, death, immigration and emigration. However, the high-resolution shifts of microbial community and mechanisms of the vertical assembly processes in marine sediments remain poorly described. Archaeal and bacterial communities were analyzed based on 16S rRNA gene amplicon sequencing and metagenomes in the Bohai Sea sediment samples. The archaeal community was dominated by Thaumarchaeota with increased alpha diversity along depth. Proteobacteria was the dominant bacterial group with decreased alpha diversity as depth increased. Sampling sites and depths collectively affected the beta-diversity for both archaeal and bacterial communities. The dominant mechanism determining archaeal community assembly was determinism, which was mostly contributed by homogeneous selection, i.e., consistent selection pressures in different locations or depths. In contrast, bacterial community assembly was dominated by stochasticity. Co-occurrence networks among different taxa and key functional genes revealed a tight community with low modularity in the bottom sediment, and disproportionately more interactions among low abundant ASVs. This suggests a significant contribution to community stabilization by rare taxa, and suggests that the bottom layer, rather than surface sediments may represent a hotspot for benthic microbial interactions.

Response of bacterial diversity and community structure to metals in mangrove sediments from South China

Human activities have given rise to metal contamination in the constituents of mangrove ecosystems, posing a critical threat to sediment microorganisms; hence, it is of great importance to comprehend the effects of metals on the microbial communities in mangrove sediments. This study was the first to explore the response of the bacterial diversity and community structure to nine metals (As, Co, Cr, Cu, Mn, Ni, Pb, V and Zn) and organic matter fractions (including total organic carbon (TOC), total nitrogen (TN), and total sulfur (TS)) in mangrove wetlands from Zhanjiang, China, using 16S rRNA high-throughput sequencing technology and Spearman correlation analysis. The results showed that these nine metals were scattered differently in different mangrove sediments, and the metals and organic matter fractions jointly affected the bacterial communities in the sediments. Several metals displayed significant positive correlations with the abundances of the phylum Bacteroidetes and the genera Actibacter and Sphingobacterium but significant negative correlations with the abundances of two genera Holophaga and Caldithrix. Furthermore, the abundances of the phylum Actinobacteria and many bacterial genera showed significant positive or negative responses to the levels of the three organic matter fractions. Interestingly, the levels of a number of bacterial genera that exhibited increased abundance with high levels of metals and TS might be reduced with high TOC and TN, and vice versa: the levels of genera that exhibited decreased abundance with high levels of metals and TS might be increased with high TOC and TN. Overall, many bacterial groups showed different response patterns to each metal or organic matter fraction, and these metals together with organic matter fractions influenced the bacterial diversity and community structure in mangrove sediments.

Effects and mechanisms of organic matter regulating the methylmercury dynamics in mangrove sediments

Mangrove ecosystems serve as an important carbon sink but also could be a hotspot that produces neurotoxic methylmercury (MeHg). Although many studies have focused on mercury (Hg) contamination in this carbon-rich ecosystem, our understanding of the effects and mechanisms of the organic matter (OM) regulation of MeHg production in mangrove sediments is still limited. Here, we examined the effects of Hg contamination and OM enrichment on MeHg production in anoxic mangrove sediments and identified the major microbial guilds attending this process. The mangrove sediments possessed a high potential for producing MeHg, but this was counterbalanced by its rapid degradation. Sulfate-reducing bacteria (SRB) such as Desulfobacterales, Desulfovibrionales, and Syntrophobacterales were the major methylators. OM diagenesis significantly changed the biogeochemical conditions, accelerating MeHg degradation in the sediments. The enhanced MeHg degradation could be attributed to the abundant sulfide produced during OM decomposition, which could potentially inhibit the Hg methylation by immobilization of inorganic Hg, abiotically degrade MeHg, and favor the non-mer-mediated degradation of MeHg by SRB. Our study provides both geochemical and microbial clues that can partly explain the low MeHg levels widely observed in mangrove sediments.

Spartina alterniflora Invaded Coastal Wetlands by Raising Soil Sulfur Contents: A Meta-Analysis

Nowadays, plant invasion has become a global ecological threat to local biodiversity and ecosystem stability. Spartina alterniflora encroaches on the ecological niches of local species and changes the soil’s nutrient cycle. However, few comprehensive assessments focus on the effects of S. alterniflora invasion. Here, we investigated how soil sulfur changed with spatiotemporal variation and life forms of native species after S. alterniflora invasion and speculated the possible mechanism of the sulfur increase based on the references. The invasion of S. alterniflora increased soil total sulfur by 57.29% and phytotoxic sulfide by 193.29%. In general, the invasion of S. alterniflora enhanced the total plant biomass and soil nutrients, e.g., soil organic carbon, total nitrogen, and soil microbial biomass carbon, further increasing soil sulfur content. The sulfur accumulation caused by S. alterniflora might result in the poisoning of native species. Thus, we hypothesized that the success of S. alterniflora invasion was closely connected with soil sulfur, especially toxic sulfide. Our study suggests that researchers should give more attention to the correlation between S. alterniflora invasion and the soil sulfur increase. More research is needed to investigate the mechanisms of the successful invasion by accumulating phytotoxic sulfide.

The importance of conditionally rare taxa for the assembly and interaction of fungal communities in mangrove sediments

The fungal communities provide the nutrients and drive the cycles of elements in nature, and the rare fungal taxa are proved to be crucial for these communities in many environments. However, the ecological functions of rare taxa for the fungal communities in mangrove ecosystems are poorly assessed until now. This work aims to reveal the importance of rare taxa for the assembly of fungal communities in mangrove sediments by using the amplicon sequencing analysis of different spatiotemporal samples collected from Sanya mangroves, China. The results showed that Ascomycota and Basidiomycota were the dominant phyla in the conditionally rare taxa (CRT). The fungal communities possessed outstanding stability against the spatiotemporal variation and most collected environmental factors. The CRT possessed narrower niches and were more affected by the environmental variables than the abundant taxa. The current work demonstrated that the CRT had significantly higher relative abundances, degrees (the number of adjacent edges), clustering coefficients, and closeness centralities in the top 8 modules of the co-occurrence network (p < 0.05), indicating the important role of the CRT for the interaction of fungal communities in mangrove sediments. These findings indicate the importance of the CRT for the fungal community structures in mangrove sediments, and would deepen our understanding of dynamic functions of mangrove fungi, thereby facilitating the management, utilization, and protection of mangrove ecosystems. KEY POINTS: • Fungal communities in mangrove sediments are stable against environment variations. • The conditionally rare taxa (CRT) possessed narrower niches than the abundant fungal taxa. • The CRT are central for the co-occurrence network and interaction of fungal communities.

Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem

Estuaries are one of the most productive ecosystems and their productivity is maintained by resident microbial communities. Recent alterations driven by climate change have further escalated these stressors leading to the propagation of traits such as antibiotic resistance and heavy metal resistance in microbial communities. Surface water samples from eleven stations along the Thakuran and Matla estuaries of the Sundarbans Biosphere Reserve (SBR) of Sundarbans mangrove located in South Asia were sampled in monsoon (June) 2019 to elucidate resident microbial communities based on Nanopore sequencing. Metagenomic analyses revealed the widespread dominance of Proteobacteria across all the stations along with a high abundance of Firmicutes. Other phyla, including Euryarchaeota, Thaumarchaeota, Actinobacteria, Bacteroidetes and Cyanobacteria showed site-specific trends in abundance. Further taxonomic affiliations showed Gammaproteobacteria and Alphaproteobacteria to be dominant classes with high abundances of Bacilli in SBR_Stn58 and SBR_Stn113. Among the eukaryotic communities, the most abundant classes included Prasinophyceae, Saccharyomycetes and Sardariomycetes. Functional annotation showed metabolic activities such as carbohydrate, amino acid, nitrogen and phosphorus metabolisms to be uniformly distributed across all the studied stations. Pathways such as stress response, sulphur metabolism and motility-associated genes appeared in low abundances in SBR. Functional traits such as antibiotic resistance showed overwhelming dominance of genes involved in multidrug resistance along with widespread resistance towards commonly used antibiotics including Tetracycline, glycopeptide and aminoglycoside. Metal resistance genes including arsenic, nickel and copper were found in comparable abundances across the studied stations. The prevalence of ARG and MRG might indicate presence of pollutants and hint toward deteriorating ecosystem health status of Sundarbans mangrove.

Microbial diversity and ecological interactions of microorganisms in the mangrove ecosystem: Threats, vulnerability, and adaptations

Mangroves are among the world's most productive ecosystems and a part of the "blue carbon" sink. They act as a connection between the terrestrial and marine ecosystems, providing habitat to countless organisms. Among these, microorganisms (e.g., bacteria, archaea, fungi, phytoplankton, and protozoa) play a crucial role in this ecosystem. Microbial cycling of major nutrients (carbon, nitrogen, phosphorus, and sulfur) helps maintain the high productivity of this ecosystem. However, mangrove ecosystems are being disturbed by the increasing concentration of greenhouse gases within the atmosphere. Both the anthropogenic and natural factors contribute to the upsurge of greenhouse gas concentration, resulting in global warming. Changing climate due to global warming and the increasing rate of human interferences such as pollution and deforestation are significant concerns for the mangrove ecosystem. Mangroves are susceptible to such environmental perturbations. Global warming, human interventions, and its consequences are destroying the ecosystem, and the dreadful impacts are experienced worldwide. Therefore, the conservation of mangrove ecosystems is necessary for protecting them from the changing environment-a step toward preserving the globe for better living. This review highlights the importance of mangroves and their microbial components on a global scale and the degree of vulnerability of the ecosystems toward anthropic and climate change factors. The future scenario of the mangrove ecosystem and the resilience of plants and microbes have also been discussed.

Mangrove microbiome reveals importance of sulfur metabolism in tropical coastal waters

Mangroves under macro-tidal regimes are global carbon sequestration hotspots but the microbial drivers of biogeochemical cycles remain poorly understood. Here, we investigate the drivers of mangrove microbial community composition across a porewater-creek-estuary-ocean continuum. Observations were performed on the Amazon region in one of the largest mangrove systems worldwide with effective sequestration of organic carbon buried in soils and dissolved carbon via outwelling to the ocean. The potential export to the adjacent oceanic region ranged from 57 to 380 kg of dissolved and particulate organic carbon per second (up to 33 thousand tons C per day). Macro tides modulated microbial communities and their metabolic processes, e.g., anoxygenic phototrophy, sulfur, and nitrogen cycling. Respiration, sulfur metabolism and dissolved organic carbon (DOC) levels were linked to functional groups and microbial cell counts. Total microbial counts decreased and cyanobacteria counts peaked in the spring tide. The microbial groups driving carbon, nitrogen, sulfur and methane cycles were consistent across all spatial scales. Taxonomic groups engaged in sulfur cycling (Allochromatium, Desulfovibrio, and Thibacillus) within mangroves were abundant at all scales. Tidally-driven porewater exchange within mangroves drove a progressive increase of sulfur cycle taxonomic groups and their functional genes both temporally (tidal cycles) and spatially (from mangrove porewater to continental shelf). Overall, we revealed a unified and consistent response of microbiomes at different spatial and temporal scales to tidally-driven mangrove porewater exchange.

Contrasting Effects of Local Environmental and Biogeographic Factors on the Composition and Structure of Bacterial Communities in Arid Monospecific Mangrove Soils

Mangrove forests are important biotic sinks of atmospheric CO2 and play an integral role in nutrient-cycling and decontamination of coastal waters, thereby mitigating climatic and anthropogenic stressors. These services are primarily regulated by the activity of the soil microbiome. To understand how environmental changes may affect this vital part of the ecosystem, it is key to understand the patterns that drive microbial community assembly in mangrove forest soils. High-throughput amplicon sequencing (16S rRNA) was applied on samples from arid Avicennia marina forests across different spatial scales from local to regional. Alongside conventional analyses of community ecology, microbial co-occurrence networks were assessed to investigate differences in composition and structure of the bacterial community. The bacterial community composition varied more strongly along an intertidal gradient within each mangrove forest, than between forests in different geographic regions (Australia/Saudi Arabia). In contrast, co-occurrence networks differed primarily between geographic regions, illustrating that the structure of the bacterial community is not necessarily linked to its composition. The local diversity in mangrove forest soils may have important implications for the quantification of biogeochemical processes and is important to consider when planning restoration activities. IMPORTANCE Mangrove ecosystems are increasingly being recognized for their potential to sequester atmospheric carbon, thereby mitigating the effects of anthropogenically driven greenhouse gas emissions. The bacterial community in the soils plays an important role in the breakdown and recycling of carbon and other nutrients. To assess and predict changes in carbon storage, it is important to understand how the bacterial community is shaped by its environment. Here, we compared the bacterial communities of mangrove forests on different spatial scales, from local within-forest to biogeographic comparisons. The bacterial community composition differed more between distinct intertidal zones of the same forest than between forests in distant geographic regions. The calculated network structure of theoretically interacting bacteria, however, differed most between the geographic regions. Our findings highlight the importance of local environmental factors in shaping the microbial soil community in mangroves and highlight a disconnect between community composition and structure in microbial soil assemblages.

Mangrove crab intestine and habitat sediment microbiomes cooperatively work on carbon and nitrogen cycling

Mangrove ecosystems, where litter and organic components are degraded and converted into detrital materials, support rich coastal fisheries resources. Sesarmid (Grapsidae) crabs, which feed on mangrove litter, play a crucial role in material flow in carbon-rich and nitrogen-limited mangrove ecosystems; however, the process of assimilation and conversion into detritus has not been well studied. In this study, we performed microbiome analyses of intestinal bacteria from three species of mangrove crab and five sediment positions in the mud lobster mounds, including the crab burrow wall, to study the interactive roles of crabs and sediment in metabolism. Metagenome analysis revealed species-dependent intestinal profiles, especially in Neosarmatium smithi, while the sediment microbiome was similar in all positions, albeit with some regional dependency. The microbiome profiles of crab intestines and sediments were significantly different in the MDS analysis based on OTU similarity; however, 579 OTUs (about 70% of reads in the crab intestinal microbiome) were identical between the intestinal and sediment bacteria. In the phenotype prediction, cellulose degradation was observed in the crab intestine. Cellulase activity was detected in both crab intestine and sediment. This could be mainly ascribed to Demequinaceae, which was predominantly found in the crab intestines and burrow walls. Nitrogen fixation was also enriched in both the crab intestines and sediments, and was supported by the nitrogenase assay. Similar to earlier reports, sulfur-related families were highly enriched in the sediment, presumably degrading organic compounds as terminal electron acceptors under anaerobic conditions. These results suggest that mangrove crabs and habitat sediment both contribute to carbon and nitrogen cycling in the mangrove ecosystem via these two key reactions.

L-Cysteine Synthase Enhanced Sulfide Biotransformation in Subtropical Marine Mangrove Sediments as Revealed by Metagenomics Analysis

High sulfides concentrations can be poisonous to environment because of anthropogenic waste production or natural occurrences. How to elucidate the biological transformation mechanisms of sulfide pollutants in the subtropical marine mangrove ecosystem has gained increased interest. Thus, in the present study, the sulfide biotransformation in subtropical mangroves ecosystem was accurately evaluated using metagenomic sequencing and quantitative polymerase chain reaction analysis. Most abundant genes were related to the organic sulfur transformation. Furthermore, an ecological model of sulfide conversion was constructed. Total phosphorus was the dominant environmental factor that drove the sulfur cycle and microbial communities. We compared mangrove and non-mangrove soils and found that the former enhanced metabolism that was related to sulfate reduction when compared to the latter. Total organic carbon, total organic nitrogen, iron, and available sulfur were the key environmental factors that effectively influenced the dissimilatory sulfate reduction. The taxonomic assignment of dissimilatory sulfate-reducing genes revealed that Desulfobacterales and Chromatiales were mainly responsible for sulfate reduction. Chromatiales were most sensitive to environmental factors. The high abundance of cysE and cysK could contribute to the coping of the microbial community with the toxic sulfide produced by Desulfobacterales. Collectively, these findings provided a theoretical basis for the mechanism of the sulfur cycle in subtropical mangrove ecosystems.

L-Cysteine Synthase Enhanced Sulfide Biotransformation in Subtropical Marine Mangrove Sediments as Revealed by Metagenomics Analysis

High sulfides concentrations can be poisonous to environment because of anthropogenic waste production or natural occurrences. How to elucidate the biological transformation mechanisms of sulfide pollutants in the subtropical marine mangrove ecosystem has gained increased interest. Thus, in the present study, the sulfide biotransformation in subtropical mangroves ecosystem was accurately evaluated using metagenomic sequencing and quantitative polymerase chain reaction analysis. Most abundant genes were related to the organic sulfur transformation. Furthermore, an ecological model of sulfide conversion was constructed. Total phosphorus was the dominant environmental factor that drove the sulfur cycle and microbial communities. We compared mangrove and non-mangrove soils and found that the former enhanced metabolism that was related to sulfate reduction when compared to the latter. Total organic carbon, total organic nitrogen, iron, and available sulfur were the key environmental factors that effectively influenced the dissimilatory sulfate reduction. The taxonomic assignment of dissimilatory sulfate-reducing genes revealed that Desulfobacterales and Chromatiales were mainly responsible for sulfate reduction. Chromatiales were most sensitive to environmental factors. The high abundance of cysE and cysK could contribute to the coping of the microbial community with the toxic sulfide produced by Desulfobacterales. Collectively, these findings provided a theoretical basis for the mechanism of the sulfur cycle in subtropical mangrove ecosystems.

Depth-dependent variability of biological nitrogen fixation and diazotrophic communities in mangrove sediments

BACKGROUND

Nitrogen-fixing prokaryotes (diazotrophs) contribute substantially to nitrogen input in mangrove sediments, and their structure and nitrogen fixation rate (NFR) are significantly controlled by environmental conditions. Despite the well-known studies on diazotrophs in surficial sediments, the diversity, structure, and ecological functions of diazotrophic communities along environmental gradients of mangrove sediment across different depths are largely unknown. Here, we investigated how biological nitrogen fixation varied with the depth of mangrove sediments from the perspectives of both NFR and diazotrophic communities.

RESULTS

Through acetylene reduction assay, nifH gene amplicon and metagenomic sequencing, we found that the NFR increased but the diversity of diazotrophic communities decreased with the depth of mangrove sediments. The structure of diazotrophic communities at different depths was largely driven by salinity and exhibited a clear divergence at the partitioning depth of 50 cm. Among diazotrophic genera correlated with NFR, Agrobacterium and Azotobacter were specifically enriched at 50-100 cm sediments, while Anaeromyxobacter, Rubrivivax, Methylocystis, Dickeya, and Methylomonas were more abundant at 0-50 cm. Consistent with the higher NFR, metagenomic analysis demonstrated the elevated abundance of nitrogen fixation genes (nifH/D/K) in deep sediments, where nitrification genes (amoA/B/C) and denitrification genes (nirK and norB) became less abundant. Three metagenome-assembled genomes (MAGs) of diazotrophs from deep mangrove sediments indicated their facultatively anaerobic and mixotrophic lifestyles as they contained genes for low-oxygen-dependent metabolism, hydrogenotrophic respiration, carbon fixation, and pyruvate fermentation.

CONCLUSIONS

This study demonstrates the depth-dependent variability of biological nitrogen fixation in terms of NFR and diazotrophic communities, which to a certain extent relieves the degree of nitrogen limitation in deep mangrove sediments. Video Abstract.

Biotechnological potential of fungi from a mangrove ecosystem: Enzymes, salt tolerance and decolorization of a real textile effluent

The mangrove is an ecosystem bounded by the line of the largest tide in size that occurs in climatic and subtropical regions. In this environment, microorganisms and their enzymes are involved in a series of transformations and nutrient cycling. To evaluate the biotechnological potential of fungi from a mangrove ecosystem, samples from mangrove trees were collected at the Paranaguá Estuarine Complex in Brazil and 40 fungal isolates were obtained, cultivated, and screened for hydrolytic and ligninolytic enzymes production, adaptation to salinity and genetic diversity. The results showed a predominance of hydrolytic enzymes and fungal tolerance to ≤ 50 g L^-1 sodium chloride (NaCl) concentration, a sign of adaptive halophilia. Through morphological and molecular analyses, the isolates were identified as: Trichoderma atroveride, Microsphaeropsis arundinis, Epicoccum sp., Trichoderma sp., Gliocladium sp., Geotrichum sp. and Cryphonectria sp. The ligninolytic enzymatic potential of the fungi was evaluated in liquid cultures in the presence and absence of seawater and the highest activity of laccase among isolates was observed in the presence of seawater with M. arundinis (LB07), which produced 1,037 U L^-1. Enzymatic extracts of M. arundinis fixed at 100 U L^-1 of laccase partially decolorized a real textile effluent in a reaction without pH adjustment and chemical mediators. Considering that mangrove fungi are still few explored, the results bring an important contribution to the knowledge about these microorganisms, as their ability to adapt to saline conditions, biodegradation of pollutants, and enzymatic potential, which make them promising candidates in biotechnological processes.

Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds

Seagrasses are marine angiosperms that can live completely or partially submerged in water and perform a variety of significant ecosystem services. Like terrestrial angiosperms, seagrasses can reproduce sexually and, the pollinated female flower develop into fruits and seeds, which represent a critical stage in the life of plants. Seed microbiomes include endophytic microorganisms that in terrestrial plants can affect seed germination and seedling health through phytohormone production, enhanced nutrient availability and defence against pathogens. However, the characteristics and origins of the seagrass seed microbiomes is unknown. Here, we examined the endophytic bacterial community of six microenvironments (flowers, fruits, and seeds, together with leaves, roots, and rhizospheric sediment) of the seagrass Halophila ovalis collected from the Swan Estuary, in southwestern Australia. An amplicon sequencing approach (16S rRNA) was used to characterize the diversity and composition of H. ovalis bacterial microbiomes and identify core microbiome bacteria that were conserved across microenvironments. Distinct communities of bacteria were observed within specific seagrass microenvironments, including the reproductive tissues (flowers, fruits, and seeds). In particular, bacteria previously associated with plant growth promoting characteristics were mainly found within reproductive tissues. Seagrass seed-borne bacteria that exhibit growth promoting traits, the ability to fix nitrogen and anti-pathogenic potential activity, may play a pivotal role in seed survival, as is common for terrestrial plants. We present the endophytic community of the seagrass seeds as foundation for the identification of potential beneficial bacteria and their selection in order to improve seagrass restoration.

Effects of heavy metals and organic matter fractions on the fungal communities in mangrove sediments from Techeng Isle, South China

Heavy metal pollution has become a serious environmental problem in mangrove ecosystems and has attracted more attention. Most of previous studies have mainly focused on the effects of heavy metals on bacterial communities in mangrove sediments. This study was the first to investigate the effects of heavy metals (e.g., As, Co, Cr, Cu, Mn, Ni, Pb, V and Zn) and organic matter fractions (including total organic carbon (TOC), total nitrogen (TN), and total sulfur (TS)) on the fungal communities in mangrove sediments from Techeng Isle, South China. The results of this study indicated that the average contents of Mn, Pb and V of 8.30-161.80 μg/g presented relatively higher pollution levels, while the concentrations of Zn, Cr, Cu and Ni of 0.80-21.93 μg/g were lower than those recorded in other mangrove ecosystems. Furthermore, the sediment fungal community structures responded differently to the nine heavy metals and three organic matter fractions. Heavy metals Cr, Pb and V displayed significant positive correlations with Eutypella (P < 0.05), whereas significant negative correlations with Cystobasidium, Lulworthia, Cladosporium, Lulwoana and Cephalotheca (P < 0.05). In addition, the effects of heavy metals and TS on many fungal genera were opposite to those of TOC and TN. Fungal genera that decreased with high TOC and TN contents may be increased with high heavy metal contents and TS, and vice versa, and the genera that increased with high TOC and TN contents may be decreased with high heavy metals and TS. Our results suggested that many heavy metals, such as Cr, Pb and V, were sensitive to several fungal genera in mangrove sediments, and heavy metals together with organic matter fractions may participate and shape the fungal communities in mangrove sediments.

Human activities can drive sulfate-reducing bacteria community in Chinese intertidal sediments by affecting metal distribution

Sulfate-reducing bacteria (SRB), which are ubiquitous in intertidal sediments, play an important role in global sulfur and carbon cycles, and in the bioremediation of toxic metalloids/metals. Pollution from human activities is now a major challenge to the sustainable development of the intertidal zone, but little is known about how and to what extent various anthropic and/or natural factors affect the SRB community. In the current study, based on the dsrB gene, we investigated the SRB community in intertidal sediment along China's coastline. The results showed that dsrB gene abundances varied among different sampling sites, with the highest average abundance of SRB at XHR (near the Bohai Sea). The SRB community structures showed obvious spatial distribution patterns with latitude along the coastal areas of China, with Desulfobulbus generally being the dominant genus. Correlation analysis and redundancy discriminant analysis revealed that total organic carbon (TOC) and pH were significantly correlated with the richness of the SRB community, and salinity, pH, sulfate and climatic parameters could be the important natural factors influencing the composition of the SRB community. Moreover, metals, especially bioavailable metals, could regulate the diversity and composition of the SRB communities. Importantly, according to structural equation model (SEM) analysis, anthropic factors (e.g., population, economy and industrial activities) could drive SRB community diversity directly or by significantly affecting the concentrations of metals. This study provides the first comprehensive investigation of the direct and indirect anthropic factors on the SRB community in intertidal sediments on a continental scale.

Candidatus Thiovulum sp. strain imperiosus: the largest free-living Epsilonproteobacteraeota Thiovulum strain lives in a marine mangrove environment

A large (47.75 ± 3.56 µm in diameter) Thiovulum bacterial strain forming white veils is described from a marine mangrove ecosystem. High sulfide concentrations (up to 8 mM of H2S) were measured on sunken organic matter (wood/bone debris) under laboratory conditions. This sulfur-oxidizing bacterium colonized the organic matter, forming a white veil. According to conventional scanning electron microscope (SEM) observations, bacterial cells are ovoid and slightly motile by numerous small flagella present on the cell surface. Large intracytoplasmic internal sulfur granules were observed, suggesting a sulfidic-based metabolism. Observations were confirmed by elemental sulfur distribution detected by energy-dispersive X-ray spectroscopy (EDXS) analysis using an environmental scanning electron microscope (ESEM) on non-dehydrated samples. Phylogenetic analysis of the partial sequence of 16S rDNA obtained from purified fractions of this Epsilonproteobacteraeota strain indicates that this bacterium belongs to the Thiovulaceae cluster and could be one of the largest Thiovulum ever described. We propose to name this species Candidatus Thiovulum sp. strain imperiosus.

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.

Long-term dynamic changes in attached and planktonic microbial communities in a contaminated aquifer

Biodegradation is responsible for most contaminant removal in plumes of organic compounds and is fastest at the plume fringe where microbial cell numbers and activity are highest. As the plume migrates from the source, groundwater containing the contaminants and planktonic microbial community encounters uncontaminated substrata on which an attached community subsequently develops. While attached microbial communities are important for biodegradation, the time needed for their establishment, their relationship with the planktonic community and the processes controlling their development are not well understood. We compare the dynamics of development of attached microbial communities on sterile substrata in the field and laboratory microcosms, sampled simultaneously at intervals over two years. We show that attached microbial cell numbers increased rapidly and stabilised after similar periods of incubation (∼100 days) in both field and microcosm experiments. These timescales were similar even though variation in the contaminant source evident in the field was absent in microcosm studies, implying that this period was an emergent property of the attached microbial community. 16S rRNA gene sequencing showed that attached and planktonic communities differed markedly, with many attached organisms strongly preferring attachment. Successional processes were evident, both in community diversity indices and from community network analysis. Community development was governed by both deterministic and stochastic processes and was related to the predilection of community members for different lifestyles and the geochemical environment.

Effect of PAHs on nitrogen-fixing and sulfate-reducing microbial communities in seagrass Enhalus acoroides sediment

Seagrass meadows are vital ecosystems with high productivity and biodiversity and often in the oligotrophic area. Nitrogen usually limits productivity in this ecosystem as the main nutrient factor. Biological nitrogen fixation by diazotrophs in the rhizosphere sediment can introduce "new" nitrogen into the ecosystem. Previous studies revealed that most sulfate-reducing bacteria (SRB) can also fix nitrogen like the nitrogen-fixing bacteria (NFB). Moreover, both sulfate reduction and nitrogen fixation were affected by the organic pollutant. However, rare information is available regarding the NFB and SRB community composition and their temporal response to the pollutant. The quantitative real-time polymerase chain reaction and polymerase chain reaction denaturing gradient gel electrophoresis have been used to analyze NFB and SRB communities' shifts under different PAHs concentrations. They both experienced a dramatic shift under PAHs stress but exhibited different patterns. SRB could use the low and high concentration PAHs at the early stage of the incubation, while only the low concentration of PAHs could stimulate the growth of NFB through the whole incubation period. The predominant species of NFB communities were Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria; while for SRB communities were class Epsilonproteobacteria. Redundancy analysis indicated the significant environmental factors for the two communities were both ammonium and pH (P < 0.05). There existed nifH sequences related to known nitrogen fixing SRB Desulfatibacillum alkenivorans, which confirmed that microbial N₂ fixation and sulfate reduction were coupled in the seagrass ecosystem by molecular technique. Our investigation provides new insight into the NFB and SRB community in the seagrass meadow.

Influence of Temperature and Sulfate Concentration on the Sulfate/Sulfite Reduction Prokaryotic Communities in the Tibetan Hot Springs

The distribution and diversity of sulfate/sulfite reduction prokaryotic (SRP) communities in hot springs from the Quzhuomu and Daggyai Geothermal Zone of Tibetan, China, was reported for the first time. In hot springs that are naturally hyperthermal and anoxic, the sulfur cycle is one of the most active cycles of the elements. The distribution of SRP in response to temperature is of great importance to the understanding of biogeochemical cycling of sulfur in geothermal features. Little is known about the SRP in geothermal zone. In this study, the diversity of SRP was investigated in the sediments from the Daggyai and Quzhuomu geothermal zone using PCR amplification, cloning and sequencing of the dissimilatory sulfite reductase beta subunit gene (dsrB). The abundance of dsrB and 16S rRNA genes, were determined by quantitative polymerase chain reactions. In addition, correlations of the SRP assemblages with environmental factors were analyzed by the aggregated boosted tree (ABT) statistical analysis. The results showed that SRP populations were diverse, but were mainly composed of Desulfobacterales, Desulfovibrionales, Syntrophobacterales, Clostridia and Nitrospirales, and large fraction (25%) of novel sequences have branched groups in the dsrB phylogenetic tree. In Quzhuomu geothermal zone, sulfate-rich hot springs are characterized by thick bacterial mats that are green or red and the SRP populations mainly appear at mid-temperature (50 °C to 70 °C). In low-sulfate hot springs in the Daggyai geothermal zone, although gray or pink streamers are widely formed at 60 °C to 80 °C, they prefer to inhabit in green mat at lower temperature (30 °C to 50 °C). With increasing temperature, the diversity of the dsrB gene at the OTU level (cutoff 97%) decreased, while its relative abundance increased. This result suggests that temperature played an important role in affecting dsrB gene distribution.

Shotgun metagenomics reveals a heterogeneous prokaryotic community and a wide array of antibiotic resistance genes in mangrove sediment

Saline tolerant mangrove forests partake in vital biogeochemical cycles. However, they are endangered due to deforestation as a result of urbanization. In this study, we have carried out a metagenomic snapshot of the mangrove ecosystem from five countries to assess its taxonomic, functional and antibiotic resistome structure. Chao1 alpha diversity varied significantly (P < 0.001) between the countries (Brazil, Saudi Arabia, China, India and Malaysia). All datasets were composed of 33 phyla dominated by eight major phyla covering >90% relative abundance. Comparative analysis of mangrove with terrestrial and marine ecosystems revealed the strongest heterogeneity in the mangrove microbial community. We also observed that the mangrove community shared similarities to both the terrestrial and marine microbiome, forming a link between the two contrasting ecosystems. The antibiotic resistant genes (ARG) resistome was comprised of nineteen level 3 classifications dominated by multidrug resistance efflux pumps (46.7 ± 4.3%) and BlaR1 family regulatory sensor-transducer disambiguation (25.2 ± 4.8%). ARG relative abundance was significantly higher in Asian countries and in human intervention datasets at a global scale. Our study shows that the mangrove microbial community and its antibiotic resistance are affected by geography as well as human intervention and are unique to the mangrove ecosystem. Understanding changes in the mangrove microbiome and its ARG is significant for sustainable development and public health.

Succession of sulfur bacteria during decomposition of cyanobacterial bloom biomass in the shallow Lake Nanhu: An ex situ mesocosm study

Previous studies of the dynamics of sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) have focused on deep stratified lakes. The objective of this study is to present an in-depth investigation of the structure and dynamics of sulfur bacteria (including SRB and SOB) in the water column of shallow freshwater lakes. A cyanobacterial bloom biomass (CBB)-amended mesocosm experiment was conducted in this study, in which water was taken from a shallow eutrophic lake with sulfate levels near 40 mg L^-1. Illumina sequencing was used to investigate SRB and SOB species involved in CBB decomposition and the effects of the increases in sulfate input on the water column microbial community structure. The accumulation of dissolved sulfide (∑H₂S) produced by SRB during CBB decomposition stimulated the growth of SOB, and ∑H₂S was then oxidized back to sulfate by SOB in the water column. Chlorobaculum sequences (the main SOB species in the study) were significantly influenced by increases in sulfate input, with relative abundance increasing approximately four-fold in treatments amended with 40 mg L^-1 sulfate (referred to as 40S) when compared to the treatment without additional sulfate addition (referred to as CU). Additionally, an increase in SOB number was observed from day 26-37, concurrent with the decrease in SRB number, indicating the succession of sulfur bacteria. These findings suggest that biological sulfur oxidation and succession of sulfur bacteria occur in the water column during CBB decomposition in shallow freshwater ecosystems, and the increases in sulfate input stimulate microbial sulfur oxidation.

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

Biological nitrogen fixation (BNF) mediated by diazotrophic communities is a major source of bioavailable nitrogen in mangrove wetlands, which plays important roles in maintaining the health and stability of mangrove ecosystems. Recent large-scale mangrove afforestation activities have drawn great attention due to introduced mangrove species and their potential impacts on bio-functionalities of local ecosystems. However, the effects of introduced mangrove species on diazotrophic communities remain unclear. Here, we analyzed rhizosphere and endosphere diazotrophic communities between native mangrove species (Avicennia marina) and introduced mangrove species (Sonneratia apetala and Laguncularia racemose) by sequencing nifH gene amplicons. Our results showed that S. apetala and L. racemose introduction significantly (P < 0.05) increased nutrition components (e.g., total carbon and total nitrogen) in rhizosphere, as well as the diazotrophs richness in rhizosphere and endosphere. The relative abundance of clusters III diazotrophs in the rhizosphere and Rhizobium in the endosphere were significantly increased with L. racemosa or S. apetala introduction. Fe and pH were the main environmental factors driving the divergence of endophyte-rhizophyte diazotrophs between native and introduced mangroves. The correlation-based network analyses indicated that the interaction among rhizophyte-endophyte diazotrophs is more harmonious in native mangrove, while there exist more competition in introduced mangroves. These findings expand our current understanding of BNF in mangrove afforestation, and providing new perspectives to sustainable management of mangrove ecosystem.

Detection of sentinel bacteria in mangrove sediments contaminated with heavy metals

Mangroves in the Northwest Coast of South America are contaminated with heavy metals due to wastewater discharges from industries, affecting the biota from this environment. However, bacteria proliferate in these harsh environmental conditions becoming possible sentinel of these contaminations. In this study, bacterial community composition was analyzed by throughput sequencing of the 16S rRNA gene from polluted and pristine mangrove sediments affected by marked differences in heavy metal concentrations. Core bacteria were dominated by Proteobacteria, Firmicutes, and Bacteroidetes phyla, with strong differences between sites at class and genus levels, correlated with metal levels. Increment of abundance on specific OTUs were associated with either elevated or decreased concentrations of metals and with the sulfur cycle. The abundance of Sulfurovum lithotrophicum, Leptolinea tardivitalis, Desulfococcus multivorans and Aminobacterium colombiense increases when metals rise. On contrary, Bacillus stamsii, Nioella nitrareducens and Clostridiisalibacter paucivorans abundance increases when metal levels are reduced. We propose these OTUs as bacterial sentinels, whose abundance can help monitor the restoration programs of contaminated mangrove sediments in the future.

Potential bacterial bioindicators of urban pollution in mangroves

Despite their ecological and socioeconomic importance, mangroves are among the most threatened tropical environments in the world. In the past two decades, the world's mangrove degradation and loss were estimated to lie between an 35% and >80%. However, appropriate bioindicators for assessing the impact of external factors, and for differentiating polluted from unpolluted areas are still scarce. Here, we determine the physicochemical profiles of the soils of two mangroves, one exposed to and one not exposed to anthropogenic factors. By metagenomic analysis based on 16S rRNA, we generated the bacterial diversity profiles of the soils and estimated their functional profiles. Our results showed that the two examined mangrove forests differed significantly in the physicochemical properties of the soils, especially regarding organic carbon, phosphorus and metal content, as well as in their microbial communities, which was likely caused by anthropogenic pollution. The physicochemical differences between the soils explained 76% of the differential bacterial composition, and 64% depended solely on gradients of phosphorus, metal ions and potassium. We found two genera JL-ETNP-Z39 and TA06 exclusively in polluted and non-polluted mangroves, respectively. Additionally, the polluted mangrove was enriched in Gemmatimonadetes, Cyanobacteria, Chloroflexi, Firmicutes, Acidobacteria, and Nitrospirae. A total of 77 genera were affected by anthropic contamination, of which we propose 33 as bioindicators; 26 enriched, and 7 depleted upon pollution.

Interactions of sulfur and methane-oxidizing bacteria in tropical estuarine sediments

The bacterial oxidation of sulfur and methane is central to the biogeochemical processes in sediments such as the tropical mangrove sediments. However, there is a lacuna of information on the seasonal interactions including the influence of monsoons which is a major driver of seasonal change, on sulfur-oxidizing bacteria (SOB) and methane-oxidizing bacteria (MOB), their activity and the environmental variables. To understand these interactions, the analysis was carried out on sediment samples that were sampled monthly for a year from Chorao mangrove, Goa, southwest coast of India. SOB (3.8×10⁵CFU g^-1) and MOB (0.90×10⁵CFU g^-1) had maximum average abundance in the surface sediments in the post-monsoon and monsoon season, respectively. The mean sulfur-oxidation activity (SOA) of 2.63 mM day^-1 and methane-oxidation activity (MOA) of 110.94 mM day^-1 were highest in surface sediments during the post-monsoon season. Generally, the activity of SOB and MOB in surface sediments of post-monsoon was 2.2 times(×) and 2.8× respectively higher than that in the monsoon season. Among the environmental parameters analyzed, protein and sulfide concentrations significantly (p < 0.001) influenced SOA and MOA, respectively. There was a significant difference in SOA (p < 0.003) and MOA (p < 0.036) in surface sediments between the monsoon and the post-monsoon season. During the monsoon season, when the system is a sink of terrestrial/anthropogenic material, the interrelationship of SOB with MOA (r = 0.617, p < 0.001) and SOB with SOA (r = 0.489, p < 0.05) aids in maintaining the homeostasis of the system.

High-throughput sequencing and analysis of microbial communities in the mangrove swamps along the coast of Beibu Gulf in Guangxi, China

Mangrove swamp is one of the world's richest and most productive marine ecosystems. This ecosystem also has a great ecological importance, but is highly susceptible to anthropogenic disturbances. The balance of mangrove ecosystem depends largely on the microbial communities in mangrove sediments. Thus, understanding how the mangrove microbial communities respond to spatial differences is essential for more accurate assessment of mangrove ecosystem health. To this end, we performed the first medium-distance (150 km) research on the biogeographic distribution of mangrove microbial communities. The hypervariable regions of 16S rRNA gene was sequenced by Illumina to compare the microbial communities in mangrove sediments collected from six locations (i.e. Zhenzhu harbor, Yuzhouping, Maowei Sea, Qinzhou harbor, Beihai city and Shankou) along the coastline of Beibu Gulf in Guangxi province, China. Collectively, Proteobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, Parvarchaeota, Acidobacteria and Cyanobacteria were the predominant phyla in the mangrove sediments of this area. At genus level, the heat map of microbial communities reflected similarities between study sites and was in agreement with their biogeographic characteristics. Interestingly, the genera Desulfococcus, Arcobacter, Nitrosopumilus and Sulfurimonas showed differences in abundance between study sites. Furthermore, the principal component analysis (PCA) and unweighted UniFrac cluster tree of beta diversity were used to study the biogeographic diversity of the microbial communities. Relatively broader variation of microbial communities was found in Beihai city and Qinzhou harbour, suggesting that environmental condition and historical events may play an important role in shaping the bacterial communities as well. This is the first report on medium-distance range distribution of bacteria in the mangrove swamp ecosystem. Our data is valuable for monitoring and evaluation of the impact of human activity on mangrove habitats from the perspective of microbiome.

Microbial community structure of soils in Bamenwan mangrove wetland

Microbial community diversity and composition are important for the maintenance of mangrove ecosystem. Bacterial and archaeal community composition of the Bamenwan Mangrove Wetland soil in Hainan, China, was determined using pyrosequencing technique. Bacterial community composition presented differences among the five soil samples. Rhizobiales with higher abundance were observed in inner mangrove forest samples, while Desulfobacterales were in the seaward edge samples, and Frankiales, Gaiellales and Rhodospirillales in the landedge sample. For archaea, Crenarchaeota and Euryarchaeota dominated in five samples, but the proportion in each samples were different. Dominant archaeal community composition at the order level was similar in the seaward edge samples. The dominant archaeal clusters in the two inner mangrove forest samples were different, with Soil Crenarchaeotic Group (SCG) and Halobacteriales in sample inside of Bruguiera sexangula forest and SCG, Methanosarcinales and Marine Benthic Group B (MBGB) in sample inside of Xylocarpus mekongensis forest. The dominant archaeal clusters in land sample were unique, with Terrestrial Group and South African Gold Mine Group 1. The metabolic pathways including metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems and human diseases were all detected for bacterial and archaeal functional profiles, but metabolic potentials among five samples were different.

Regional and Microenvironmental Scale Characterization of the Zostera muelleri Seagrass Microbiome

Seagrasses are globally distributed marine plants that represent an extremely valuable component of coastal ecosystems. Like terrestrial plants, seagrass productivity and health are likely to be strongly governed by the structure and function of the seagrass microbiome, which will be distributed across a number of discrete microenvironments within the plant, including the phyllosphere, the endosphere and the rhizosphere, all different in physical and chemical conditions. Here we examined patterns in the composition of the microbiome of the seagrass Zostera muelleri, within six plant-associated microenvironments sampled across four different coastal locations in New South Wales, Australia. Amplicon sequencing approaches were used to characterize the diversity and composition of bacterial, microalgal, and fungal microbiomes and ultimately identify "core microbiome" members that were conserved across sampling microenvironments. Discrete populations of bacteria, microalgae and fungi were observed within specific seagrass microenvironments, including the leaves and roots and rhizomes, with "core" taxa found to persist within these microenvironments across geographically disparate sampling sites. Bacterial, microalgal and fungal community profiles were most strongly governed by intrinsic features of the different seagrass microenvironments, whereby microscale differences in community composition were greater than the differences observed between sampling regions. However, our results showed differing strengths of microbial preferences at the plant scale, since this microenvironmental variability was more pronounced for bacteria than it was for microalgae and fungi, suggesting more specific interactions between the bacterial consortia and the seagrass host, and potentially implying a highly specialized coupling between seagrass and bacterial metabolism and ecology. Due to their persistence within a given seagrass microenvironment, across geographically discrete sampling locations, we propose that the identified "core" microbiome members likely play key roles in seagrass physiology as well as the ecology and biogeochemistry of seagrass habitats.

Exploring bacterial functionality in mangrove sediments and its capability to overcome anthropogenic activity

Mangrove forests are highly productive yet vulnerable ecosystems that act as important carbon sinks ("blue carbon"). The objective of this work was to analyze the impact of anthropogenic activities on microbiome structure and functioning. The metagenomic analysis revealed that the taxonomic compositions were grossly similar across all mangrove microbiomes. Remarkably, these microbiomes, along the gradient of anthropogenic impact, showed fluctuations in the relative abundances of bacterial taxa predicted to be involved in sulfur cycling processes. Functions involved in sulfur metabolism, such as APS pathways (associated with sulfate reduction and sulfur oxidation processes) were prevalent across the microbiomes, being sox and dsrAB genes highly expressed on anthropogenically-impacted areas. Apparently, the oil-impacted microbiomes were more affected in taxonomic than in functional terms, as high functional redundancies were noted across them. The microbial gene diversity found was typical for a functional system, even following the previous disturbance.

Fiddler crab bioturbation determines consistent changes in bacterial communities across contrasting environmental conditions

Ecosystem functions are regulated by compositional and functional traits of bacterial communities, shaped by stochastic and deterministic processes. Biogeographical studies have revealed microbial community taxonomy in a given ecosystem to change alongside varying environmental characteristics. Considering that stable functional traits are essential for community stability, we hypothesize that contrasting environmental conditions affect microbial taxonomy rather than function in a model system, testing this in three geographically distinct mangrove forests subjected to intense animal bioturbation (a shared deterministic force). Using a metabarcoding approach combined with sediment microprofiling and biochemistry, we examined vertical and radial sediment profiles of burrows belonging to the pantropical fiddler crab (subfamily Gelasiminae) in three contrasting mangrove environments across a broad latitudinal range (total samples = 432). Each mangrove was environmentally distinct, reflected in taxonomically different bacterial communities, but communities consistently displayed the same spatial stratification (a halo effect) around the burrow which invariably determined the retention of similar inferred functional community traits independent of the local environment.