Seagrass vegetation affect the vertical organization of microbial communities in sediment

Specialists regulate microbial network and community assembly in subtropical seagrass sediments under differing land use conditions

Microorganisms in the sediment play a pivotal role in the functioning and stability of seagrass ecosystems and their dynamics are influenced by the nutrient acquisition strategies of host plants. While the distinct impacts of microbial generalists and specialists on community dynamics are recognized, their distribution patterns and ecological roles within seagrass ecosystems remain largely unexplored. To address this issue, we conducted an analysis of community assembly processes and co-occurrence relationships of both microbial generalists and specialists within sediment profiles (0-100 cm) from seagrass habitats subjected to differing land use conditions. The results revealed that seagrasses in Yifeng Estuary experienced the large proportion of cultivated land and exhibited higher organic carbon content in the 0-20 cm surface sediment layer. Nitrogen-cycling bacteria were predominantly associated with seagrasses from Yifeng Estuary, whereas Vibrio spp. was more prevalent in seagrasses from Liusha Bay. Notably, seagrass Halophia beccarii (YHB) in Yifeng Estuary harbored higher niche breadths for both microbial generalist and specialist compared to Halodule uninervis (LHU) and Halophia ovalis (LHO) from Liusha Bay. Stochastic processes were pivotal in shaping seagrass sediment microbial communities, with a higher immigration rate observed in YHB, suggesting greater microbial turnover in this area. Additionally, YHB sediment presented lower drift and higher dispersal limitation among generalists compared to LHU and LHO, whereas the pattern was reversed among specialists. Specialists were found to play a crucial role in shaping microbial interactions within YHB sediment, with genera Halioglobus identified as keystone species in the network. The specialists were further found to significantly influence microbial β-diversity in seagrass sediment directly. Overall, our findings illustrated how microbial generalists and specialists were distributed in seagrass sediments in response to land use changes and provided new insights into the potential roles of microbial regulation in degraded seagrass ecosystems.

Occurrence and distribution of antibiotic pollution and antibiotic resistance genes in seagrass meadow sediments based on metagenomics

Seagrass meadows are one of the most important coastal ecosystems that provide essential ecological and economic services. The contamination levels of antibiotic and antibiotic resistance genes (ARGs) in coastal ecosystems are severely elevated owing to anthropogenic disturbances, such as terrestrial input, aquaculture effluent, and sewage discharge. However, few studies have focused on the occurrence and distribution of antibiotics and their corresponding ARGs in this habitat. Thus, we investigated the antibiotic and ARGs profiles, microbial communities, and ARG-carrying host bacteria in typical seagrass meadow sediments collected from Swan Lake, Caofeidian shoal harbor, Qingdao Bay, and Sishili Bay in the Bohai Sea and northern Yellow Sea. The total concentrations of 30 detected antibiotics ranged from 99.35 to 478.02 μg/kg, tetracyclines were more prevalent than other antibiotics. Metagenomic analyses showed that 342 ARG subtypes associated with 22 ARG types were identified in the seagrass meadow sediments. Multidrug resistance genes and RanA were the most dominant ARG types and subtypes, respectively. Co-occurrence network analysis revealed that Halioglobus, Zeaxanthinibacter, and Aureitalea may be potential hosts at the genus level, and the relative abundances of these bacteria were higher in Sishili Bay than those in other areas. This study provided important insights into the pollution status of antibiotics and ARGs in typical seagrass meadow sediments. Effective management should be performed to control the potential ecological health risks in seagrass meadow ecosystems.

Microbial Detoxification of Sediments Underpins Persistence of Zostera marina Meadows

Eelgrass meadows have attracted much attention not only for their ability to maintain marine ecosystems as feeding grounds for marine organisms but also for their potential to store atmospheric and dissolved CO2 as blue carbon. This study comprehensively evaluated the bacterial and chemical data obtained from eelgrass sediments of different scales along the Japanese coast to investigate the effect on the acclimatization of eelgrass. Regardless of the eelgrass habitat, approximately 1% Anaerolineales, Babeliales, Cytophagales, and Phycisphaerales was present in the bottom sediment. Sulfate-reducing bacteria (SRB) were present at 3.69% in eelgrass sediment compared to 1.70% in bare sediment. Sulfur-oxidizing bacteria (SOB) were present at 2.81% and 1.10% in the eelgrass and bare sediment, respectively. Bacterial composition analysis and linear discriminant analysis revealed that SOB detoxified H2S in the eelgrass meadows and that the larger-scale eelgrass meadows had a higher diversity of SOB. Our result indicated that there were regional differences in the system that detoxifies H2S in eelgrass meadows, either microbial oxidation mediated by SOB or O2 permeation via the physical diffusion of benthos. However, since bacterial flora and phylogenetic analyses cannot show bias and/or causality due to PCR, future kinetic studies on microbial metabolism are expected.

A pilot restoration of Enhalus acoroides by transplanting dislodged rhizome fragments and its effect on the microbial diversity of submarine sediments

Enhalus acoroides, the largest seagrass species in terms of morphology, has been observed to be declining significantly. In an effort to restore seagrass meadows, we conducted a transplantion utilizing dislodged rhizome fragments of E. acoroides as the donor materials. The growth of transplanted seagrass was monitored over a period of three years, and the impact of seagrass recolonization on sedimentary environment was assessed through analysis of sediment microbial diversity. The transplanted plants displayed notable growth, resulting in the successful recolonization of experimental plots by seagrass. The 3-year data also revealed the following findings: 1) the new shoot recruitment rate (per year) (NSR) of transplanted seagrass was 2.33 in the first year, 1.36 in the second year, and 0.83 in the third year, indicating a rapid initial growth rate of E. acoroides that subsequently slowed down; 2) the numbers of shoots and aboveground biomass of transplanted seagrass had increased by 13.0 and 15.9-fold, respectively, whereas only 3.3 and 5.3-fold increases of the natural seagrass were observed, suggesting that the transplantation of seagrass leads to a significantly accelerated recovery compared to its natural regeneration process. Furthermore, the restoration of E. acoroides resulted in a higher microbial diversity in the submarine sediments within the restoration area, as compared to the adjacent unvegetated area. This suggests that the re-vegetation of E. acoroides has a positive influence on the overall health of the sedimentary environment. This study strongly advocates for the active transplantation of dislodged E. acoroides plants resulting from human activities as a potential approach for future coastal management, specifically for the restoration of E. acoroides meadows.

Identification of anthropogenic source of Pb and Cd within two tropical seagrass species in South China: Insight from Pb and Cd isotopes

Seagrass beds are susceptible to deterioration and heavy metals represent a crucial impact factor. The accumulation of heavy metal in two tropical seagrass species were studied in South China in this study and multiple methods were used to identify the heavy metal sources. E. acoroides (Enhalus acoroides) and T. hemperichii (Thalassia hemperichii) belong to the genus of Enhalus and Thalassia in the Hydrocharitaceae family, respectively. Heavy metal concentrations in the two seagrasses followed the order of Cr > Zn > Cu > Ni > As > Pb > Co > Cd based on the whole plant, and their bioconcentration factors were 31.8 ± 29.3 (Cr), 5.7 ± 1.3 (Zn), 7.0 ± 3.8 (Cu), 3.0 ± 1.9 (Ni), 1.2 ± 0.3 (As), 1.7 ± 0.9 (Pb), 9.1 ± 11.1 (Co) and 2.8 ± 0.6 (Cd), indicating the intense enrichment in Co and Cr within the two seagrasses. The two seagrasses were prone to accumulate all the listed heavy metals (except for As in E. acoroides), especially Co (BCFs of 1124) and Cr (BCFs of 2689) in the aboveground parts, and the belowground parts of both seagrasses also accumulated most metals (BCFs of 27) excluding Co and Pb. The Pb isotopic ratios (mean 208Pb/204Pb, 207Pb/204Pb and 206Pb/204Pb values of 38.2054, 15.5000 and 18.3240, respectively) and Cd isotopic compositions (δ114/110Cd values ranging from -0.09‰ to 0.58‰) within seagrasses indicated the anthropogenic sources of Pb and Cd including coal combustion, traffic emissions and agricultural activities. This study described the absorption characteristics of E. acoroides and T. hemperichii to some heavy metals, and further demonstrated the successful utilization of Pb and Cd isotopes as discerning markers to trace anthropogenic origins of heavy metals (mainly Pb and Cd) in seagrasses. Pb and Cd isotopes can mutually verify and be helpful to understand more information in pollution sources and improve the reliability of conclusion deduced from concentrations or a single isotope.

Epiphytic and endophytic microbiome of the seagrass Zostera marina: Do they contribute to pathogen reduction in seawater?

Seagrass meadows provide crucial ecosystem services for coastal environments and were shown to reduce the abundance of waterborne pathogens linked to infections in humans and marine organisms in their vicinity. Among potential drivers, seagrass phenolics released into seawater have been linked to pathogen suppression, but the potential involvement of the seagrass microbiome has not been investigated. We hypothesized that the microbiome of the eelgrass Zostera marina, especially the leaf epiphytes that are at direct interface between the seagrass host and the surrounding seawater, inhibit waterborne pathogens thereby contributing to their removal. Using a culture-dependent approach, we isolated 88 bacteria and fungi associated with the surfaces and inner tissues of the eelgrass leaves (healthy and decaying) and the roots. We assessed the antibiotic activity of microbial extracts against a large panel of common aquatic, human (fecal) and plant pathogens, and mined the metabolome of the most active extracts. The healthy leaf epibiotic bacteria, particularly Streptomyces sp. strain 131, displayed broad-spectrum antibiotic activity superior to some control drugs. Gram-negative bacteria abundant on healthy leaf surfaces, and few endosphere-associated bacteria and fungi also displayed remarkable activities. UPLC-MS/MS-based untargeted metabolomics analyses showed rich specialized metabolite repertoires with low annotation rates, indicating the presence of many undescribed antimicrobials in the extracts. This study contributes to our understanding on microbial and chemical ecology of seagrasses, implying potential involvement of the seagrass microbiome in suppression of pathogens in seawater. Such effect is beneficial for the health of ocean and human, especially in the context of climate change that is expected to exacerbate all infectious diseases. It may also assist future seagrass conservation and management strategies.

Macrophytes and their wrack as a habitat for faecal indicator bacteria and Vibrio in coastal marine environments

Waterborne pathogenic bacteria, including faecal indicator bacteria and potentially pathogenic Vibrio, are a global concern for diseases transmitted through water. A systematic review was conducted to analyse publications that investigated these bacteria in relation to macrophytes (seagrasses and macroalgae) in coastal marine environments. The highest quantities of FIB were found on brown algae and seagrasses, and the highest quantities of Vibrio bacteria were on red algae. The most extensively studied macrophyte group was brown algae, green algae were the least researched. Macrophyte wrack was found to favor the presence of FIB, but there is a lack of information about Vibrio quantities in this environment. To understand the role of Vibrio bacteria that are pathogenic to humans, molecular methods complementary to cultivation methods should be used. Further research is needed to understand the underlying mechanisms of FIB and potentially pathogenic Vibrio with macrophytes and their microbiome in the coastal marine environment.

Studies on the Composition and Diversity of Seagrass Ruppia sinensis Rhizosphere Mmicroorganisms in the Yellow River Delta

Seagrass is a significant primary producer of coastal ecosystems; however, the continued degradation of seagrass beds is a serious problem that has attracted widespread attention from researchers. Rhizosphere microorganisms affect seagrass and participate in many life activities of seagrass. This study explored the relationship between the composition of microbes in the rhizosphere and the surrounding environment of Ruppia sinensis by using High-throughput sequencing methods. The dominant bacterial groups in the rhizosphere surface sediments of R. sinensis and the surrounding environment are Proteobacteria, Bacteroidota, and Firmicutes. Moreover, the dominant fungal groups are Ascomycota, Basidiomycota, and Chytridiomycota. Significant differences (p < 0.05) were identified in microbial communities among different groups (rhizosphere, bulk sediment, and surrounding seawater). Seventy-four ASVs (For bacteria) and 48 ASVs (For fungal) were shared among seagrass rhizosphere, surrounding sediment, and seawater. The rhizosphere was enriched in sulfate-reducing bacteria and nitrogen-fixing bacteria. In general, we obtained the rhizosphere microbial community of R. sinensis, which provided extensive evidence of the relative contribution of the seagrass rhizosphere and the surrounding environment.

Changes in the Rhizosphere Prokaryotic Community Structure of Halodule wrightii Monospecific Stands Associated to Submarine Groundwater Discharges in a Karstic Costal Area

Belowground seagrass associated microbial communities regulate biogeochemical dynamics in the surrounding sediments and influence seagrass physiology and health. However, little is known about the impact of environmental stressors upon interactions between seagrasses and their prokaryotic community in coastal ecosystems. Submerged groundwater discharges (SGD) at Dzilam de Bravo, Yucatán, Mexico, causes lower temperatures and salinities with higher nutrient loads in seawater, resulting in Halodule wrightii monospecific stands. In this study, the rhizospheric archaeal and bacterial communities were characterized by 16S rRNA Illumina sequencing along with physicochemical determinations of water, porewater and sediment in a 400 m northwise transect from SGD occurring at 300 m away from coastline. Core bacterial community included Deltaproteobacteria, Bacteroidia and Planctomycetia, possibly involved in sulfur metabolism and organic matter degradation while highly versatile Bathyarchaeia was the most abundantly represented class within the archaeal core community. Beta diversity analyses revealed two significantly different clusters as result of the environmental conditions caused by SGD. Sites near to SGD presented sediments with higher redox potentials and sand contents as well as lower organic matter contents and porewater ammonium concentrations compared with the furthest sites. Functional profiling suggested that denitrification, aerobic chemoheterotrophy and environmental adaptation processes could be better represented in these sites, while sulfur metabolism and genetic information processing related profiles could be related to SGD uninfluenced sites. This study showed that the rhizospheric prokaryotic community structure of H. wrightii and their predicted functions are shaped by environmental stressors associated with the SGD. Moreover, insights into the archaeal community composition in seagrasses rhizosphere are presented.

Year-around survey and manipulation experiments reveal differential sensitivities of soil prokaryotic and fungal communities to saltwater intrusion in Florida Everglades wetlands

Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased episodic or chronic saltwater exposure, leading to shifts in biogeochemistry, plant- and microbial communities, as well as ecological services. Yet, it is still difficult to predict how soil microbial communities respond to the saltwater exposure because of poorly understood microbial sensitivity within complex wetland soil microbial communities, as well as the high spatial and temporal heterogeneity of wetland soils and saltwater exposure. To address this, we first conducted a two-year survey of microbial community structure and bottom water chemistry in submerged surface soils from 14 wetland sites across the Florida Everglades. We identified ecosystem-specific microbial biomarker taxa primarily associated with variation in salinity. Bacterial, archaeal and fungal community composition differed between freshwater, mangrove, and marine seagrass meadow sites, irrespective of soil type or season. Especially, methanogens, putative denitrifying methanotrophs and sulfate reducers shifted in relative abundance and/or composition between wetland types. Methanogens and putative denitrifying methanotrophs declined in relative abundance from freshwater to marine wetlands, whereas sulfate reducers showed the opposite trend. A four-year experimental simulation of saltwater intrusion in a pristine freshwater site and a previously saltwater-impacted site corroborated the highest sensitivity and relative increase of sulfate reducers, as well as taxon-specific sensitivity of methanogens, in response to continuously pulsing of saltwater treatment. Collectively, these results suggest that besides increased salinity, saltwater-mediated increased sulfate availability leads to displacement of methanogens by sulfate reducers even at low or temporal salt exposure. These changes of microbial composition could affect organic matter degradation pathways in coastal freshwater wetlands exposed to sea-level rise, with potential consequences, such as loss of stored soil organic carbon.

A Tight Interaction between the Native Seagrass Cymodocea nodosa and the Exotic Halophila stipulacea in the Aegean Sea Highlights Seagrass Holobiont Variations

Seagrasses harbour bacterial communities with which they constitute a functional unit called holobiont that responds as a whole to environmental changes. Epiphytic bacterial communities rapidly respond to both biotic and abiotic factors, potentially contributing to the host fitness. The Lessepsian migrant Halophila stipulacea has a high phenotypical plasticity and harbours a highly diverse epiphytic bacterial community, which could support its invasiveness in the Mediterranean Sea. The current study aimed to evaluate the Halophila/Cymodocea competition in the Aegean Sea by analysing each of the two seagrasses in a meadow zone where these intermingled, as well as in their monospecific zones, at two depths. Differences in holobionts were evaluated using seagrass descriptors (morphometric, biochemical, elemental, and isotopic composition) to assess host changes, and 16S rRNA gene to identify bacterial community structure and composition. An Indicator Species Index was used to identify bacteria significantly associated with each host. In mixed meadows, native C. nodosa was shown to be affected by the presence of exotic H. stipulacea, in terms of both plant descriptors and bacterial communities, while H. stipulacea responded only to environmental factors rather than C. nodosa proximity. This study provided evidence of the competitive advantage of H. stipulacea on C. nodosa in the Aegean Sea and suggests the possible use of associated bacterial communities as an ecological seagrass descriptor.

Exploring the variation of bacterial community and nitrogen transformation functional genes under the pressure of heavy metals in different coastal mariculture patterns

Equilibrium in microbial dynamics and nitrogen transformation in the sediment is critical for maintaining healthy mariculture environment. However, our understanding about the impact of heavy metals on the bacterial community and nitrogen transformation functional genes in different mariculture patterns is still limited. Here, we analyzed 30 sediment samples in the vertical distribution from three different mariculture patterns mainly include open mariculture zone (K), closed mariculture pond (F) and pristine marine area (Q). Illumina MiSeq Sequencing was applied to investigate the bacterial community and structure in the sediment. Quantitative polymerase chain reaction (qPCR) was used to determine the effect of heavy metals on nitrogen transformation functional genes. Results showed that bacterial community and structure varied greatly in different mariculture patterns. Chloroflexi, Proteobacteria and Desulfobacterota were predominant phyla in the coastal mariculture area. High concentrations of heavy metals mainly enriched in the up layer (5-40 cm) of the sediment in the mariculture zone. The abundance of functional genes in the closed mariculture pond was much higher than the open mariculture zone and pristine marine area. And the high abundance of nitrification and denitrification functional genes mainly accumulated at the depth from 5 cm to 40 cm. Heavy metals content such as Fe, Cr, Mn, Ni, As, Cd, Pb and nutrient content NH₄⁺-N, NO₃^--N and NO₂^--N were highly associated with bacterial community and nitrogen transformation functional genes. This study comprehensively elaborated the effect of heavy metals on the bacterial community and nitrogen transformation functional genes in different coastal mariculture patterns, indicating the possible role of closed mariculture pond in reducing nitrogen transformation efficiency, which will provide useful information for preventing pollution risk in the mariculture area.

Seagrasses and local environment control the bacterial community structure and carbon substrate utilization in brackish sediments

Seagrasses are complex benthic coastal ecosystems that play a crucial role in organic matter cycling and carbon sequestration. However, little is known about how seagrasses influence the structure and carbon utilization potential of benthic bacterial communities. This study examined the bacterial communities in monospecific and mixed meadows of seagrasses and compared with bulk (unvegetated) sediments from Chilika, a brackish water coastal lagoon of India. High-throughput sequencing of 16S rRNA genes revealed a vegetation effect in terms of differences in benthic bacterial community diversity, composition, and abundances in comparison with bulk sediments. Desulfobacterales, Chromatiales, Enterobacteriales, Clostridiales, Vibrionales, and Acidimicrobiales were major taxa that contributed to differences between seagrass and bulk sediments. Seagrasses supported ∼5.94 fold higher bacterial abundances than the bulk due to rich organic carbon stock in their sediments. Co-occurrence network demonstrated much stronger potential interactions and connectedness in seagrass bacterial communities compared to bulk. Chromatiales and Acidimicrobiales were identified as the top two keystone taxa in seagrass bacterial communities, whereas, Dehalococcoidales and Rhizobiales were in bulk communities. Seagrasses and local environmental factors, namely, water depth, water pH, sediment salinity, redox potential, total organic carbon, available nitrogen, sediment texture, sediment pH, and sediment core depth were the major drivers of benthic bacterial community composition. Carbon metabolic profiling revealed that heterotrophic bacteria in seagrass sediments were much more metabolically diverse and active than bulk. The utilization of carbon substrate guilds, namely, amino acids, amines, carboxylic acids, carbohydrates, polymers, and phenolic compounds was enhanced in seagrass sediments. Metabolic mapping predicted higher prevalence of sulfate-reducer and N₂ fixation metabolic functions in seagrass sediments. Overall, this study showed that seagrasses control benthic bacterial community composition and diversity, enhance heterotrophic carbon substrate utilization, and play crucial roles in organic matter cycling including degradation of hydrocarbon and xenobiotics in coastal sediments.

Seagrass Colonization Alters Diversity, Abundance, Taxonomic, and Functional Community Structure of Benthic Microbial Eukaryotes

Seagrass form high productive ecosystems in coastal environments. However, the effects of these coastal plants on the structure and function of the belowground eukaryotic microbiome remain elusive. In this study, we characterized the community of microbial eukaryotes (microeukaryotes) in both vegetated and unvegetated sediments using 18S rRNA gene amplicon sequencing and quantitative PCR. Analysis of sequencing data showed that the eelgrass (Zostera marina) colonization decreased the alpha diversity indices of benthic microeukaryotes. Apicomplexa represented an average of 83% of reads across all samples, with a higher proportion at the vegetated sites. The taxonomic community structure was significantly different between these two types of sediments, for which the concentration ofNH 4 + in sediment porewater and salinity could account. Phylogenetic analyses of long 18S rRNA genes (around 1,030 bp) indicated these apicomplexan parasites are closely related to gregarine Lecudina polymorpha. Determination of 18S rRNA gene abundances provided evidence that the eelgrass markedly promoted the biomass of the gregarine and all microeukaryotes in the seagrass-colonized sediments and confirmed that the gregarine was hosted by a polychaete species. Significantly higher gene abundances of heterotrophs and mixotrophs were found at the vegetated sites, which could be explained by the finer sediments and short supply of dissolved inorganic nitrogen, respectively. The pigmented protists were more abundant in 18S rRNA gene copies at the lower and higher pH levels than at the intermediate. Nevertheless, the fractions of heterotrophs and phototrophs in the community were significantly related to porewater N:P ratio. These results indicate that seagrass colonization significantly induces an increase in overall biomass and a decrease in diversity of benthic microeukaryotes, making them more heterotrophic. This study also highlights that the hotspot of eukaryotic parasites could be linked with the high productivity of a natural ecosystem.

Functional trait responses of macrobenthic communities in seagrass microhabitats of a temperate lagoon

Understanding the effects of habitat heterogeneity on the functioning of macrobenthic communities is essential to the conservation of biodiversity in coastal ecosystems. However, the effects of habitat heterogeneity on the functional trait composition and diversity of seagrass bed macrobenthos are as scarce. In the present study, functional diversity indices (i.e., functional dispersion, functional richness, and Rao's quadratic entropy), RLQ analysis, and fourth-corner analysis indicated that macrobenthic functional trait composition and diversity differ among seagrass bed microhabitats (interior, edge, and bare sediment). More specifically, functional traits were more evenly distributed in the seagrass bed interior and edge habitats, when compared to bare sediment, and functional diversity was significantly higher (p < 0.01). Functional trait distributions were influenced by environmental parameters (e.g., total organic carbon, organic matter, and grain size). Suspension-feeding and burrowing bivalves preferentially inhabited bare sediment with high sand content and low TOC, whereas herbivorous, small, and sensitive species mainly inhabited muddy sediments with higher organic supply.

An overview and assessment of the existing technological options for management and resource recovery from beach wrack and dredged sediments: An environmental and economic perspective

The present work discusses the problems and management options of beach wrack and dredged sediments. Beach wrack and dredged sediments near the shores have affected the coastal ecosystem, badly. The piles of beach wrack residues might be a significant emitter of greenhouse gases (GHGs) and dredged sediment is a substantial source of heavy metals and other pollutants. The recovery of valuable resources such as metals and nutrients from these so-called "wastes" is a sustainable strategy to enhance the resilience of the coastal ecosystem and management. The beach wrack meadows can be a potential source for green energy production. Even the demand for biodegradable polymers can be supplied by utilizing the waste beach wracks. The residues of beach wrack species like Posidonia oceanica, Zostera marina, Ulva spc. and Enhalus acorodies can be very beneficial species in terms of economic growth. Red algae have been the most favored and efficient candidate for methane yield. In case of dredged sediment, dewatering of sediment is an essential step for successful resource extraction. Although, extraction methods are almost similar to that applied for soil treatment, which includes pretreatment, physical partitioning, washing, thermal treatment, biological extraction, and immobilization. The fractionation study can be a beneficial tool for determining the metal species present in the sediment. Immobilization techniques are successful but continuous monitoring is required. The vitrification technique is highly effective but very expensive. Thermal treatment is useful for volatile metals such as mercury (Hg), but costs are high. Biological extractions are comparatively cheap but time-consuming. Henceforth, very few extraction methods are available for sediment and required further advancement in this field.

Metatranscriptomics reveals different features of methanogenic archaea among global vegetated coastal ecosystems

Vegetated coastal ecosystems (VCEs; i.e., mangroves, saltmarshes, and seagrasses) represent important sources of natural methane emission. Despite recent advances in the understanding of novel taxa and pathways associated with methanogenesis in these ecosystems, the key methanogenic players and the contribution of different substrates to methane formation remain elusive. Here, we systematically investigate the community and activity of methanogens using publicly available metatranscriptomes at a global scale together with our in-house metatranscriptomic dataset. Taxonomic profiling reveals that 13 groups of methanogenic archaea were transcribed in the investigated VCEs, and they were predominated by Methanosarcinales. Among these VCEs, methanogens exhibited all the three known methanogenic pathways in some mangrove sediments, where methylotrophic methanogens Methanosarcinales/Methanomassiliicoccales grew on diverse methyl compounds and coexisted with hydrogenotrophic (mainly Methanomicrobiales) and acetoclastic (mainly Methanothrix) methanogens. Contrastingly, the predominant methanogenic pathway in saltmarshes and seagrasses was constrained to methylotrophic methanogenesis. These findings reveal different archaeal methanogens in VCEs and suggest the potentially distinct methanogenesis contributions in these VCEs to the global warming.

Heavy metal accumulation and ecological risk on four seagrass species in South China

Zn, Pb, Cr, Cu, Ni, Cd concentration and ecological risk were studied in three bays to evaluate the heavy metal (HM) contamination of seagrasses. Seasonal HM accumulation varied according to locations, seagrass species and tissues. Halophila beccarii had much higher HM concentrations except for Cr in Zhelin Bay, however, bioconcentration factors (BCF) of Cu, Ni, Pb, Zn were higher in Liusha than Zhelin Bay. Cr was much enriched in Thalassia hemperichii and Enhalus acoroides than Halophila beccarii and Halophila ovalis. Cr, Cu, Ni, Pb were easy to accumulate in belowground tissues in Halophila ovalis. In contrast, almost all HM were more enriched in aboveground tissues in other species. Generally, BCF exceeding 1 and high metal pollution index suggested HM had potential ecological risk on seagrasses. The results provide the reference for managing and protecting seagrass ecosystem in South China, and are significant to expand the global seagrass detection network.

Seasonal Dynamics of Bathyarchaeota-Dominated Benthic Archaeal Communities Associated with Seagrass (Zostera japonica) Meadows

Little is known about the seasonal dynamic of archaeal communities and their potential ecological functions in temperate seagrass ecosystems. In this study, seasonal changes in diversity, community structure, and potential metabolic functions of benthic archaea in surface sediments of two seagrass meadows along the northern Bohai Sea in China were investigated using Miseq sequencing of the 16S rRNA gene and Tax4Fun2 functional prediction. Overall, Crenarchaeota (mainly Bathy-15, Bathy-8, and Bathy-6) dominated, followed by Thermoplasmatota, Asgardarchaeota, and Halobacterota, in terms of alpha diversities and relative abundance. Significant seasonal changes in the entire archaeal community structure were observed. The major phyla Methanobacteria, Nitrosopumilales, and genus Methanolobus had higher proportions in spring, while MBG-D and Bathyarchaeota were more abundant in summer and autumn, respectively. Alpha diversities (Shannon and Simpson) were the highest in summer and the lowest in autumn (ANOVA test, p < 0.05). Salinity, total organic carbon, and total organic nitrogen were the most significant factors influencing the entire archaeal community. Higher cellulose and hemicellulose degradation potentials occurred in summer, while methane metabolism potentials were higher in winter. This study indicated that season had strong effects in modulating benthic archaeal diversity and functional potentials in the temperate seagrass ecosystems.

Spatial and Species Variations of Bacterial Community Structure and Putative Function in Seagrass Rhizosphere Sediment

Seagrasses are an important part of the coral reef ecosystem, and their rhizosphere microbes are of great ecological importance. However, variations in diversity, composition, and potential functions of bacterial communities in the seagrass rhizosphere of coral reef ecosystems remain unclear. This study employed the high-throughput sequencing based on 16S rDNA gene sequences and functional annotation of prokaryotic taxa (FAPROTAX) analysis to investigate these variations based on seagrass species and sampling locations, respectively. Results demonstrated that the seagrass rhizosphere microbial community was mainly dominated by phylum Proteobacteria (33.47%), Bacteroidetes (23.33%), and Planctomycetes (12.47%), while functional groups were mainly composed of sulfate respiration (14.09%), respiration of sulfur compounds (14.24%), aerobic chemoheterotrophy (20.87%), and chemoheterotrophy (26.85%). Significant differences were evident in alpha diversity, taxonomical composition and putative functional groups based on seagrass species and sampling locations. Moreover, the core microbial community of all investigated samples was identified, accounting for 63.22% of all obtained sequences. Network analysis indicated that most microbes had a positive correlation (82.41%), and two module hubs (phylum Proteobacteria) were investigated. Furthermore, a significant positive correlation was found between the OTUs numbers obtained and the functional groups assigned for seagrass rhizosphere microbial communities (p < 0.01). Our result would facilitate future investigation of the function of seagrass rhizosphere microbes.

The Seagrass Holobiont: What We Know and What We Still Need to Disclose for Its Possible Use as an Ecological Indicator

Microbes and seagrass establish symbiotic relationships constituting a functional unit called the holobiont that reacts as a whole to environmental changes. Recent studies have shown that the seagrass microbial associated community varies according to host species, environmental conditions and the host’s health status, suggesting that the microbial communities respond rapidly to environmental disturbances and changes. These changes, dynamics of which are still far from being clear, could represent a sensitive monitoring tool and ecological indicator to detect early stages of seagrass stress. In this review, the state of art on seagrass holobiont is discussed in this perspective, with the aim of disentangling the influence of different factors in shaping it. As an example, we expand on the widely studied Halophila stipulacea’s associated microbial community, highlighting the changing and the constant components of the associated microbes, in different environmental conditions. These studies represent a pivotal contribution to understanding the holobiont’s dynamics and variability pattern, and to the potential development of ecological/ecotoxicological indices. The influences of the host’s physiological and environmental status in changing the seagrass holobiont, alongside the bioinformatic tools for data analysis, are key topics that need to be deepened, in order to use the seagrass-microbial interactions as a source of ecological information.