The Microbial Communities of Leaves and Roots Associated with Turtle Grass (Thalassia testudinum) and Manatee Grass (Syringodium filliforme) are Distinct from Seawater and Sediment Communities, but Are Similar between Species and Sampling Sites

Handwashing basins and healthcare associated infections: Bacterial diversity in biofilms on faucets and drains

BACKGROUND

Increasingly, hospital handwashing basins have been identified as a source of healthcare-associated infections. Biofilms formed on the faucet and drains of handbasins can potentially harbour pathogenic microbes and promote the dissemination of antimicrobial resistance. However, little is known about the diversity of these biofilm communities and the routes of contamination.

AIM

The aim of this paper was to use 16S rRNA gene amplicon sequencing to investigate the diversity of prokaryote communities present in faucet and drain biofilm samples taken from hospital and residential handbasins.

FINDINGS

The biofilm prokaryotes communities were diverse, with high abundances of potentially corrosive, biofilm forming and pathogenic genera, including those that are not typically waterborne. The β-diversity showed statistically significant differences in the variation of bacterial communities on the basis on building type (hospital vs residential p = 0.0415). However, there was no statistically significant clustering based on sampling site (faucet vs drain p = 0.46). When examining the β-diversity between individual factors, there was a significant difference between drain biofilms of different buildings (hospital drain vs residential drain p = 0.0338).

CONCLUSION

This study demonstrated that biofilms from hospital and residential handbasins contain complex and diverse microbial communities that differ significantly by building type. It also showed biofilms formed on the faucet and drain of a hospital's handbasins were not significantly different. Future research is needed to understand the potential mechanisms of transfer between drains and faucets of hospital handbasins. This information will inform improved infection control guidelines to control this underrecognized source of infections.

Impacts of eutrophication on microbial community structure in sediment, seawater, and phyllosphere of seagrass ecosystems

Introduction

Seagrass-associated microbial communities play a crucial role in the growth and health of seagrasses. However, like seagrass meadows, seagrass-associated microbial communities are often affected by eutrophication. It remains unclear how eutrophication influences the composition and function of microbial communities associated with different parts of seagrass.

Methods

We employed prokaryotic 16S rRNA gene high-throughput sequencing combining microbial community structure analysis and co-occurrence network analysis to investigate variances in microbial community compositions, potential functions and complexities across sediment, seagrass leaves, and seawater within different eutrophic areas of two adjacent seagrass meadows on Hainan Island, China.

Results

Our results indicated that microbial diversity on seagrass leaves was significantly lower than in sediment but significantly higher than in seawater. Both sediment and phyllosphere microbial diversity showed no significant difference between the highly eutrophic and less eutrophic sites in each lagoon. However, sediment microbial diversity was higher in the more eutrophic lagoon, while phyllosphere microbial diversity was higher in the less eutrophic lagoon. Heavy eutrophication increased the relative abundance of phyllosphere microorganisms potentially involved in anaerobic metabolic processes, while reducing those responsible for beneficial functions like denitrification. The main factor affecting microbial diversity was organic carbon in seawater and sediment, with high organic carbon levels leading to decreased microbial diversity. The co-occurrence network analysis revealed that heavy eutrophication notably reduced the complexity and internal connections of the phyllosphere microbial community in comparison to the sediment and seawater microbial communities. Furthermore, ternary analysis demonstrated that heavy eutrophication diminished the external connections of the phyllosphere microbial community with the sediment and seawater microbial communities.

Conclusion

The pronounced decrease in biodiversity and complexity of the phyllosphere microbial community under eutrophic conditions can lead to greater microbial functional loss, exacerbating seagrass decline. This study emphasizes the significance of phyllosphere microbial communities compared to sediment microbial communities in the conservation and restoration of seagrass meadows under eutrophic conditions.

Microbiomes of Thalassia testudinum throughout the Atlantic Ocean, Caribbean Sea, and Gulf of Mexico are influenced by site and region while maintaining a core microbiome

Plant microbiomes are known to serve several important functions for their host, and it is therefore important to understand their composition as well as the factors that may influence these microbial communities. The microbiome of Thalassia testudinum has only recently been explored, and studies to-date have primarily focused on characterizing the microbiome of plants in a single region. Here, we present the first characterization of the composition of the microbial communities of T. testudinum across a wide geographical range spanning three distinct regions with varying physicochemical conditions. We collected samples of leaves, roots, sediment, and water from six sites throughout the Atlantic Ocean, Caribbean Sea, and the Gulf of Mexico. We then analyzed these samples using 16S rRNA amplicon sequencing. We found that site and region can influence the microbial communities of T. testudinum, while maintaining a plant-associated core microbiome. A comprehensive comparison of available microbial community data from T. testudinum studies determined a core microbiome composed of 14 ASVs that consisted mostly of the family Rhodobacteraceae. The most abundant genera in the microbial communities included organisms with possible plant-beneficial functions, like plant-growth promoting taxa, disease suppressing taxa, and nitrogen fixers.

Network Analysis Indicates Microbial Assemblage Differences in Life Stages of Cladophora

Cladophora represents a microscopic forest that provides many ecological niches and fosters a diverse microbiota. However, the microbial community on Cladophora in brackish lakes is still poorly understood. In this study, the epiphytic bacterial communities of Cladophora in Qinghai Lake were investigated at three life stages (attached, floating, and decomposing). We found that in the attached stage, Cladophora was enriched with chemoheterotrophic and aerobic microorganisms, including Yoonia-Loktanella and Granulosicoccus. The proportion of phototrophic bacteria was higher in the floating stage, especially Cyanobacteria. The decomposing stage fostered an abundance of bacteria that showed vertical heterogeneity from the surface to the bottom. The surface layer of Cladophora contained mainly stress-tolerant chemoheterotrophic and photoheterotrophic bacteria, including Porphyrobacter and Nonlabens. The microbial community in the middle layer was similar to that of floating-stage Cladophora. Purple oxidizing bacteria were enriched in the bottom layer, with Candidatus Chloroploca, Allochromatium, and Thiocapsa as the dominant genera. The Shannon and Chao1 indices of epibiotic bacterial communities increased monotonically from the attached stage to the decomposing stage. Microbial community composition and functional predictions indicate that a large number of sulfur cycle-associated bacteria play an important role in the development of Cladophora. These results suggest that the microbial assemblage on Cladophora in a brackish lake is complex and contributes to the cycling of materials. IMPORTANCE Cladophora represents a microscopic forest that provides many ecological niches fostering a diverse microbiota, with a complex and intimate relationship between Cladophora and bacteria. Many studies have focused on the microbiology of freshwater Cladophora, but the composition and succession of microorganisms in different life stages of Cladophora, especially in brackish water, have not been explored. In this study, we investigated the microbial assemblages in the life stages of Cladophora in the brackish Qinghai Lake. We show that heterotrophic and photosynthetic autotrophic bacteria are enriched in attached and floating Cladophora, respectively, whereas the epiphytic bacterial community shows vertical heterogeneity in decomposing mats.

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.

The metamicrobiome: key determinant of the homeostasis of nutrient recycling

The metamicrobiome is an integrated concept to study carbon and nutrient recycling in ecosystems. Decomposition of plant-derived matter by free-living microbes and fire - two key recycling pathways - are highly sensitive to global change. Mutualistic associations of microbes with plants and animals strongly reduce this sensitivity. By solving a fundamental allometric trade-off between metabolic and homeostatic capacity, these mutualisms enable continued recycling of plant matter where and when conditions are unfavourable for the free-living microbiome. A diverse metamicrobiome - where multiple plant- and animal-associated microbiomes complement the free-living microbiome - thus enhances homeostasis of ecosystem recycling rates in variable environments. Research into metamicrobiome structure and functioning in ecosystems is therefore important for progress towards understanding environmental change.

Microbial communities on eelgrass (Zostera marina) thriving in Tokyo Bay and the possible source of leaf-attached microbes

Zostera marina (eelgrass) is classified as one of the marine angiosperms and is widely distributed throughout much of the Northern Hemisphere. The present study investigated the microbial community structure and diversity of Z. marina growing in Futtsu bathing water, Chiba prefecture, Japan. The purpose of this study was to provide new insight into the colonization of eelgrass leaves by microbial communities based on leaf age and to compare these communities to the root-rhizome of Z. marina, and the surrounding microenvironments (suspended particles, seawater, and sediment). The microbial composition of each sample was analyzed using 16S ribosomal gene amplicon sequencing. Each sample type was found to have a unique microbial community structure. Leaf-attached microbes changed in their composition depending on the relative age of the eelgrass leaf. Special attention was given to a potential microbial source of leaf-attached microbes. Microbial communities of marine particles looked more like those of eelgrass leaves than those of water samples. This finding suggests that leaf-attached microbes were derived from suspended particles, which could allow them to go back and forth between eelgrass leaves and the water column.

Particle-attached Microbes in Eelgrass Vegetation Areas Differ in Community Structure Depending on the Distance from the Eelgrass Bed

Zostera marina (eelgrass) is a submerged flowering plant often found in the coastal areas of Japan. Large amounts of suspended particles form in highly productive environments, such as eelgrass beds, and the behavior of these particles is expected to affect the surrounding microbial community. We investigated the microbial community structure of suspended particles in three eelgrass fields (Ikuno-Shima Is., Mutsu Bay, and Nanao Bay) and inferred the formation and dynamics of suspended particles from a microbial community structure ana-lysis. Seawater samples were collected directly above each eelgrass bed (eelgrass-covering) and from locations dozens of meters away from the eelgrass bed (bare-ground). In consideration of the two different lifestyles of marine microbes, microbial communities were obtained from particle-attached (PA) and free-living (FL) states. Differences in microbial diversity and community structures were observed between PA and FL in all eelgrass beds. The FL microbial community was similar between the two sampling points (eelgrass-covering and bare-ground), whereas a significant difference was noted in the microbial community structure of suspended particles between the two sampling points. This difference appeared to be due to the supply of organic matter from the eelgrass sea ground and leaf-attached detritus produced by microbial activity. In addition, the classes Flavobacteriia, Alphaproteobacteria, and Gammaproteobacteria were abundant in the PA and FL fractions. Furthermore, many sequences of the key groups (e.g., Planctomycetes and Verrucomicrobia) were exclusively detected in the PA fraction, in which they may circulate nutrients. The present results provide insights into the microbial communities of suspended particles and provide the first step towards understanding their biogeochemical impact on the eelgrass bed.

Composition and Structural Characteristics of Rhizosphere Microorganisms of Polygonum sibiricum (Laxm.) Tzvelev in the Yellow River Delta

The Polygonum sibiricum (Laxm.) Tzvelev, an important herbal species used to protect seawalls, has a solid resistance to salinity and alkali and can grow on alkali spots in saline–alkali soils. So far, the composition, population, and characteristics of its rhizosphere biological community related to the adaptation salt–alkali environment were still unknown. In the present study, rhizosphere and non-rhizosphere soil samples from the P. sibiricum on Chenier Island were collected. High-throughput sequencing was conducted to obtain the structural diversity of rhizosphere microbial communities. Our results showed that the dominant bacteria groups in the rhizosphere and non-rhizosphere were Proteobacteria, Actinobacteriota, Gemmatimonadota, and Actinobacteriota. The dominant fungi groups in the rhizosphere and non-rhizosphere soil samples were Ascomycota, Basidiomycota, Chytridiomycota, and Mortierellomycota. The results of the ASVs (amplicon sequence variants) showed that fungi have more ASVs in common. The PERMANOVA analysis showed that the bacteria among different groups were significantly different. The PCoA (principal coordinates analysis) study also showed that the structures of the bacterial and fungal communities between the rhizosphere and non-rhizosphere were distinct. Function results showed that the relative abundance in COG (Clusters of Orthologous Groups of proteins) functional annotation was significantly different between the two groups. In addition to the general function prediction and carbohydrate transport and metabolism, the COG of the non-rhizosphere was higher than that of the rhizosphere. Our findings benefited the knowledge for studying and conserving the molecule-level adaptive mechanisms of P. sibiricum.

Factors structuring microbial communities in highly impacted coastal marine sediments (Mar Menor lagoon, SE Spain)

Coastal marine lagoons are environments highly vulnerable to anthropogenic pressures such as agriculture nutrient loading or runoff from metalliferous mining. Sediment microorganisms, which are key components in the biogeochemical cycles, can help attenuate these impacts by accumulating nutrients and pollutants. The Mar Menor, located in the southeast of Spain, is an example of a coastal lagoon strongly altered by anthropic pressures, but the microbial community inhabiting its sediments remains unknown. Here, we describe the sediment prokaryotic communities along a wide range of environmental conditions in the lagoon, revealing that microbial communities were highly heterogeneous among stations, although a core microbiome was detected. The microbiota was dominated by Delta- and Gammaproteobacteria and members of the Bacteroidia class. Additionally, several uncultured groups such as Asgardarchaeota were detected in relatively high proportions. Sediment texture, the presence of Caulerpa or Cymodocea, depth, and geographic location were among the most important factors structuring microbial assemblages. Furthermore, microbial communities in the stations with the highest concentrations of potentially toxic elements (Fe, Pb, As, Zn, and Cd) were less stable than those in the non-contaminated stations. This finding suggests that bacteria colonizing heavily contaminated stations are specialists sensitive to change.

Alterations of endophytic microbial community function in Spartina alterniflora as a result of crude oil exposure

The 2010 Deepwater Horizon disaster remains one of the largest oil spills in history. This event caused significant damage to coastal ecosystems, the full extent of which has yet to be fully determined. Crude oil contains toxic heavy metals and substances such as polycyclic aromatic hydrocarbons that are detrimental to some microbial species and may be used as food and energy resources by others. As a result, oil spills have the potential to cause significant shifts in microbial communities. This study assessed the impact of oil contamination on the function of endophytic microbial communities associated with saltmarsh cordgrass (Spartina alterniflora). Soil samples were collected from two locations in coastal Louisiana, USA: one severely affected by the Deepwater Horizon oil spill and one relatively unaffected location. Spartina alterniflora seedlings were grown in both soil samples in greenhouses, and GeoChip 5.0 was used to evaluate the endophytic microbial metatranscriptome shifts in response to host plant oil exposure. Oil exposure was associated with significant shifts in microbial gene expression in functional categories related to carbon cycling, virulence, metal homeostasis, organic remediation, and phosphorus utilization. Notably, significant increases in expression were observed in genes related to metal detoxification with the exception of chromium, and both significant increases and decreases in expression were observed in functional gene subcategories related to hydrocarbon metabolism. These findings show that host oil exposure elicits multiple changes in gene expression from their endophytic microbial communities, producing effects that may potentially impact host plant fitness.

Cable bacteria at oxygen-releasing roots of aquatic plants: a widespread and diverse plant-microbe association

Cable bacteria are sulfide-oxidising, filamentous bacteria that reduce toxic sulfide levels, suppress methane emissions and drive nutrient and carbon cycling in sediments. Recently, cable bacteria have been found associated with roots of aquatic plants and rice (Oryza sativa). However, the extent to which cable bacteria are associated with aquatic plants in nature remains unexplored. Using newly generated and public 16S rRNA gene sequence datasets combined with fluorescence in situ hybridisation, we investigated the distribution of cable bacteria around the roots of aquatic plants, encompassing seagrass (including seagrass seedlings), rice, freshwater and saltmarsh plants. Diverse cable bacteria were found associated with roots of 16 out of 28 plant species and at 36 out of 55 investigated sites, across four continents. Plant-associated cable bacteria were confirmed across a variety of ecosystems, including marine coastal environments, estuaries, freshwater streams, isolated pristine lakes and intensive agricultural systems. This pattern indicates that this plant-microbe relationship is globally widespread and neither obligate nor species specific. The occurrence of cable bacteria in plant rhizospheres may be of general importance to vegetation vitality, primary productivity, coastal restoration practices and greenhouse gas balance of rice fields and wetlands.

Metagenomic insights into the effects of submerged plants on functional potential of microbial communities in wetland sediments

Submerged plants in wetlands play important roles as ecosystem engineers to improve self-purification and promote elemental cycling. However, their effects on the functional capacity of microbial communities in wetland sediments remain poorly understood. Here, we provide detailed metagenomic insights into the biogeochemical potential of microbial communities in wetland sediments with and without submerged plants (i.e., Vallisneria natans). A large number of functional genes involved in carbon (C), nitrogen (N) and sulfur (S) cycling were detected in the wetland sediments. However, most functional genes showed higher abundance in sediments with submerged plants than in those without plants. Based on the comparison of annotated functional genes in the N and S cycling databases (i.e., NCycDB and SCycDB), we found that genes involved in nitrogen fixation (e.g., nifD/H/K/W), assimilatory nitrate reduction (e.g., nasA and nirA), denitrification (e.g., nirK/S and nosZ), assimilatory sulfate reduction (e.g., cysD/H/J/N/Q and sir), and sulfur oxidation (e.g., glpE, soeA, sqr and sseA) were significantly higher (corrected p < 0.05) in vegetated vs. unvegetated sediments. This could be mainly driven by environmental factors including total phosphorus, total nitrogen, and C:N ratio. The binning of metagenomes further revealed that some archaeal taxa could have the potential of methane metabolism including hydrogenotrophic, acetoclastic, and methylotrophic methanogenesis, which are crucial to the wetland methane budget and carbon cycling. This study opens a new avenue for linking submerged plants with microbial functions, and has further implications for understanding global carbon, nitrogen and sulfur cycling in wetland ecosystems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-021-00100-3.

Diversity and Composition of Microbial Communities in an Eelgrass (Zostera marina) Bed in Tokyo Bay, Japan

Zostera marina (eelgrass) is a widespread seagrass species that forms diverse and productive habitats along coast lines throughout much of the northern hemisphere. The present study investigated the microbial consortia of Z. marina growing at Futtsu clam-digging beach, Chiba prefecture, Japan. The following environmental samples were collected: sediment, seawater, plant leaves, and the root-rhizome. Sediment and seawater samples were obtained from three sampling points: inside, outside, and at the marginal point of the eelgrass bed. The microbial composition of each sample was analyzed using 16S ribosomal gene amplicon sequencing. Microbial communities on the dead (withered) leaf surface markedly differed from those in sediment, but were similar to those in seawater. Eelgrass leaves and surrounding seawater were dominated by the bacterial taxa Rhodobacterales (Alphaproteobacteria), whereas Rhodobacterales were a minor group in eelgrass sediment. Additionally, we speculated that the order Sphingomonadales (Alphaproteobacteria) acts as a major degrader during the decomposition process and constantly degrades eelgrass leaves, which then spread into the surrounding seawater. Withered eelgrass leaves did not accumulate on the surface sediment because they were transported out of the eelgrass bed by wind and residual currents unique to the central part of Tokyo Bay.

Seasonal Dynamics of Epiphytic Microbial Communities on Marine Macrophyte Surfaces

Surfaces of marine macrophytes are inhabited by diverse microbial communities. Most studies focusing on epiphytic communities of macrophytes did not take into account temporal changes or applied low sampling frequency approaches. The seasonal dynamics of epiphytic microbial communities was determined in a meadow of Cymodocea nodosa invaded by Caulerpa cylindracea and in a monospecific settlement of C. cylindracea at monthly intervals. For comparison the ambient prokaryotic picoplankton community was also characterized. At the OTU level, the microbial community composition differed between the ambient water and the epiphytic communities exhibiting host-specificity. Also, successional changes were observed connected to the macrophyte growth cycle. Taxonomic analysis, however, showed similar high rank taxa (phyla and classes) in the ambient water and the epiphytic communities, with the exception of Desulfobacterota, which were only found on C. cylindracea. Cyanobacteria showed seasonal changes while other high rank taxa were present throughout the year. In months of high Cyanobacteria presence the majority of cyanobacterial sequences were classified as Pleurocapsa. Phylogenetic groups present throughout the year (e.g., Saprospiraceae, Rhodobacteraceae, members without known relatives within Gammaproteobacteria, Desulfatitalea, and members without known relatives within Desulfocapsaceae) constituted most of the sequences, while less abundant taxa showed seasonal patterns connected to the macrophyte growth cycle. Taken together, epiphytic microbial communities of the seagrass C. nodosa and the macroalga C. cylindracea appear to be host-specific and contain taxa that undergo successional changes.

Characterization and Comparison of Bacterial Communities of an Invasive and Two Native Caribbean Seagrass Species Sheds Light on the Possible Influence of the Microbiome on Invasive Mechanisms

Invasive plants, including marine macrophytes, are one of the most important threats to biodiversity by displacing native species and organisms depending on them. Invasion success is dependent on interactions among living organisms, but their study has been mostly limited to negative interactions while positive interactions are mostly underlooked. Recent studies suggested that microorganisms associated with eukaryotic hosts may play a determinant role in the invasion process. Along with the knowledge of their structure, taxonomic composition, and potential functional profile, understanding how bacterial communities are associated with the invasive species and the threatened natives (species-specific/environmentally shaped/tissue-specific) can give us a holistic insight into the invasion mechanisms. Here, we aimed to compare the bacterial communities associated with leaves and roots of two native Caribbean seagrasses (Halodule wrightii and Thalassia testudinum) with those of the successful invader Halophila stipulacea, in the Caribbean island Curaçao, using 16S rRNA gene amplicon sequencing and functional prediction. Invasive seagrass microbiomes were more diverse and included three times more species-specific core OTUs than the natives. Associated bacterial communities were seagrass-specific, with higher similarities between natives than between invasive and native seagrasses for both communities associated with leaves and roots, despite their strong tissue differentiation. However, with a higher number of OTUs in common, the core community (i.e., OTUs occurring in at least 80% of the samples) of the native H. wrightii was more similar to that of the invader H. stipulacea than T. testudinum, which could reflect more similar essential needs (e.g., nutritional, adaptive, and physiological) between native and invasive, in contrast to the two natives that might share more environment-related OTUs. Relative to native seagrass species, the invasive H. stipulacea was enriched in halotolerant bacterial genera with plant growth-promoting properties (like Halomonas sp. and Lysinibacillus sp.) and other potential beneficial effects for hosts (e.g., heavy metal detoxifiers and quorum sensing inhibitors). Predicted functional profiles also revealed some advantageous traits on the invasive species such as detoxification pathways, protection against pathogens, and stress tolerance. Despite the predictive nature of our findings concerning the functional potential of the bacteria, this investigation provides novel and important insights into native vs. invasive seagrasses microbiome. We demonstrated that the bacterial community associated with the invasive seagrass H. stipulacea is different from native seagrasses, including some potentially beneficial bacteria, suggesting the importance of considering the microbiome dynamics as a possible and important influencing factor in the colonization of non-indigenous species. We suggest further comparison of H. stipulacea microbiome from its native range with that from both the Mediterranean and Caribbean habitats where this species has a contrasting invasion success. Also, our new findings open doors to a more in-depth investigation combining meta-omics with bacterial manipulation experiments in order to confirm any functional advantage in the microbiome of this invasive seagrass.

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 Second Skin of Seagrass Leaves: A Comparison of Microalgae Epiphytic Communities Between Two Different Species Across Two Seagrass Meadows in Lesser Sunda Islands

Epiphytes as the important features in the seagrass ecosystems have been studied widely, and their functions as a primary producer, influence rates of herbivory grazer, and prevent seagrass leaf from desiccation is well known. However, patterns and distribution among seagrasses especially in Indonesia, which was known as hotspot marine biodiversity is not well understood. Therefore, this study aimed to examined epiphytic assemblages on two seagrass species with different morphological and longevity, Enhalus acoroides and Cymodocea rotundata, in two different meadows (conservation area and non-conservation area) in Lesser Sunda Islands (Bali and Lombok). A total of 22 taxa of microalgae epiphytes species were identified from eight sites and 2 different species of seagrass. The highest number of collected species between class was from Bacillariophyceae (18), followed by Cyanophyceae (3) and Fragilariophyceae (1). Analysis of similarity (ANOSIM) revealed a significant difference of microalgae epiphytes assemblages between sites and seagrasses. Epiphytes assemblages in conservation area were more abundant than non-conservation area, both in Bali and Lombok. On seagrass comparison, Enhalus acoroides showed higher abundance of epiphytes assemblages than those on Cymodocea rotundata. Based on principal component analysis (PCA), this study highlights the microalgae epiphytic communities strongly influenced by seawater temperature, phosphate's concentration, and pH in sediment. This study also demonstrated that the assemblages of microalgae epiphytic communities affected by differences of seagrass morphological and longevity.

The Microbiome of the Reef Macroalga Sargassum ilicifolium in Singapore

The large canopy-forming macroalga, Sargassum ilicifolium, provides shelter and food for numerous coral reef species, but it can also be detrimental at high abundances where it outcompetes other benthic organisms for light and space. Here, we investigate the microbial communities associated with S. ilicifolium in Singapore, where it is an abundant and important member of coral reef communities. We collected eight complete S. ilicifolium thalli from eight island locations along an approximate 14 km east-to-west transect. Each thallus was dissected into three separate parts: holdfast, vesicles, and leaves. We then characterized the bacterial communities associated with each part via polymerase chain reaction (PCR) amplification of the 16S rRNA gene V4 region. We then inferred predicted metagenome functions using METAGENassist. Despite the comparatively short distances between sample sites, we show significant differences in microbial community composition, with communities further differentiated by part sampled. Holdfast, vesicles and leaves all harbor distinct microbial communities. Functional predictions reveal some separation between holdfast and leaf communities, with higher representation of sulphur cycling taxa in the holdfast and higher representation of nitrogen cycling taxa in the leaves. This study provides valuable baseline data that can be used to monitor microbial change, and helps lay the foundation upon which we can begin to understand the complexities of reef-associated microbial communities and the roles they play in the functioning and diversity of marine ecosystems.

Composition of seagrass phyllosphere microbial communities suggests rapid environmental regulation of community structure

Recent studies have revealed that seagrass blade surfaces, also known as the phyllosphere, are rich habitats for microbes; however, the primary drivers of composition and structure in these microbial communities are largely unknown. This study utilized a reciprocal transplant approach between two sites with different environmental conditions combined with 16S rRNA gene sequencing (iTag) to examine the relative influence of environmental conditions and host plant on phyllosphere community composition of the seagrass Thalassia testudinum. After 30 days, identity of phyllosphere microbial community members was more similar within the transplant sites than between despite differences in the source of host plant. Additionally, the diversity and evenness of these communities was significantly different between the two sites. These results indicated that local environmental conditions can be a primary driver in structuring seagrass phyllosphere microbial communities over relatively short time scales. Composition of microbial community members in this study also deviated from those in previous seagrass phyllosphere studies with a higher representation of candidate bacterial phyla and archaea than previously observed. The capacity for seagrass phyllosphere microbial communities to shift dramatically with environmental conditions, including ecosystem perturbations, could significantly affect seagrass-microbe interactions in ways that may influence the health of the seagrass host.

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.

Recovery and Community Succession of the Zostera marina Rhizobiome after Transplantation

Seagrasses can form mutualisms with their microbiomes that facilitate the exchange of energy sources, nutrients, and hormones and ultimately impact plant stress resistance. Little is known about community succession within the belowground seagrass microbiome after disturbance and its potential role in the plant's recovery after transplantation. We transplanted Zostera marina shoots with and without an intact rhizosphere and cultivated plants for 4 weeks while characterizing microbiome recovery and effects on plant traits. Rhizosphere and root microbiomes were compositionally distinct, likely representing discrete microbial niches. Furthermore, microbiomes of washed transplants were initially different from those of sod transplants and recovered to resemble an undisturbed state within 14 days. Conspicuously, changes in the microbial communities of washed transplants corresponded with changes in the rhizosphere sediment mass and root biomass, highlighting the strength and responsive nature of the relationship between plants, their microbiome, and the environment. Potential mutualistic microbes that were enriched over time include those that function in the cycling and turnover of sulfur, nitrogen, and plant-derived carbon in the rhizosphere environment. These findings highlight the importance and resilience of the seagrass microbiome after disturbance. Consideration of the microbiome will have meaningful implications for habitat restoration practices.IMPORTANCE Seagrasses are important coastal species that are declining globally, and transplantation can be used to combat these declines. However, the bacterial communities associated with seagrass rhizospheres and roots (the microbiome) are often disturbed or removed completely prior to transplantation. The seagrass microbiome benefits seagrasses through metabolite, nutrient, and phytohormone exchange and contributes to the ecosystem services of seagrass meadows by cycling sulfur, nitrogen, and carbon. This experiment aimed to characterize the importance and resilience of the seagrass belowground microbiome by transplanting Zostera marina with and without intact rhizospheres and tracking microbiome and plant morphological recovery over 4 weeks. We found the seagrass microbiome to be resilient to transplantation disturbance, recovering after 14 days. Additionally, microbiome recovery was linked with seagrass morphology, coinciding with increases in the rhizosphere sediment mass and root biomass. The results of this study can be used to include microbiome responses in informing future restoration work.

Host-Specificity and Core Taxa of Seagrass Leaf Microbiome Identified Across Tissue Age and Geographical Regions

The seagrass Zostera marina is a widespread foundational species in temperate coastal ecosystems that supports diverse communities of epiphytes and grazers. Bacteria link the production of seagrass to higher trophic levels and are thought to influence seagrass biology and health. Yet, we lack a clear understanding of the factors that structure the seagrass microbiome, or whether there is a consistent microbial community associated with seagrass that underpins functional roles. We sampled surface microbiome (epibiota) from new and old growth seagrass leaves and the surrounding seawater in eight meadows among four regions along the Central Coast of British Columbia, Canada to assess microbiome variability across space and as leaves age. We found that the seagrass leaf microbiome differs strongly from seawater. Microbial communities in new and old growth leaves are different from each other and from artificial seagrass leaves we deployed in one meadow. The microbiome on new leaves is less diverse and there is a small suite of core OTUs (operational taxonomic units) consistently present across regions. The overall microbial community for new leaves is more dispersed but with little regional differentiation, while the epiphytes on old leaves are regionally distinct. Many core OTUs on old leaves are commonly associated with marine biofilms. Together these observations suggest a stronger role for host filtering in new compared to old leaves, and a stronger influence of the environment and environmental colonization in old leaves. We found 11 core microbial taxa consistently present on old and new leaves and at very low relative abundance on artificial leaves and in the water column. These 11 taxa appear to be strongly associated with Z. marina. These core taxa may perform key functions important for the host such as detoxifying seagrass waste products, enhancing plant growth, and controlling epiphyte cover.

Microeukaryotic Communities Associated With the Seagrass Zostera marina Are Spatially Structured

Epibiotic microorganisms link seagrass productivity to higher trophic levels, but little is known about the processes structuring these communities, and which taxa consistently associate with seagrass. We investigated epibiotic microeukaryotes on seagrass (Zostera marina) leaves, substrates, and planktonic microeukaryotes in ten meadows in the Northeast Pacific. Seagrass epibiotic communities are distinct from planktonic and substrate communities. We found sixteen core microeukaryotes, including dinoflagellates, diatoms, and saprotrophic stramenopiles. Some likely use seagrass leaves as a substrate, others for grazing, or they may be saprotrophic organisms involved in seagrass decomposition or parasites; their relatives have been previously reported from marine sediments and in association with other hosts such as seaweeds. Core microeukaryotes were spatially structured, and none were ubiquitous across meadows. Seagrass epibiota were more spatially structured than planktonic communities, mostly due to spatial distance and changes in abiotic conditions across space. Seawater communities were relatively more similar in composition across sites and more influenced by the environmental component, but more variable over time. Core and transient taxa were both mostly structured by spatial distance and the abiotic environment, with little effect of host attributes, further indicating that those core taxa would not show a strong specific association with Z. marina.

Microbial community shift under exposure of dredged sediments from a eutrophic bay

Microbial communities occur in almost every habitat. To evaluate the homeostasis disruption of in situ microbiomes, dredged sediments from Guanabara Bay-Brazil (GB) were mixed with sediments from outside of the bay (D) in three different proportions (25%, 50%, and 75%) which we called GBD25, GBD50, and GBD75. Grain size, TOC, and metals-as indicators of complex contamination-dehydrogenase (DHA) and esterase enzymes (EST)-as indicators of microbial community availability-were determined. Microbial community composition was addressed by amplifying the 16S rRNA gene for DGGE analysis and sequencing using MiSeq platform (Illumina).We applied the quality ratio index (QR) to the GB, D, and every GBD mixture to integrate geochemical parameters with our microbiome data. QR indicated high environmental risk for GB and every GBD mixture, and low risk for D. The community shifted from aerobic to anaerobic profile, consistent with the characteristics of GB. Sample D was dominated by JTB255 marine benthic group, related to low impacted areas. Milano-WF1B-44 was the most representative of GB, often found in anaerobic and sulfur enriched environments. In GBD, the denitrifying sulfur-oxidizing bacteria, Sulfurovum, was the most representative, typically found in suboxic or anoxic niches. The canonical correspondence analysis was able to explain 60% of the community composition variation and exhibit the decrease of environmental quality as the contamination increases. Physiological and taxonomic shifts of the microbial assemblage in sediments were inferred by QR, which was suitable to determine sediment risk. The study produced sufficient information to improve the dredging plan and management.

Host and environmental determinants of microbial community structure in the marine phyllosphere

Although seagrasses are economically and ecologically critical species, little is known about their blade surface microbial communities and how these communities relate to the plant host. To determine microbial community composition and diversity on seagrass blade surfaces and in the surrounding seawater,16S rRNA gene sequencing (iTag) was used for samples collected at five sites along a gradient of freshwater input in the northern Gulf of Mexico on three separate sampling dates. Additionally, seagrass surveys were performed and environmental parameters were measured to characterize host characteristics and the abiotic conditions at each site. Results showed that Thalassia testudinum (turtle grass) blades hosted unique microbial communities that were distinct in composition and diversity from the water column. Environmental conditions, including water depth, salinity, and temperature, influenced community structure as blade surface microbial communities varied among sites and sampling dates in correlation with changes in environmental parameters. Microbial community composition also correlated with seagrass host characteristics, including growth rates and blade nutrient composition. There is some evidence for a core community for T. testudinum as 21 microorganisms from five phyla (Cyanobacteria, Proteobacteria, Planctomycetes, Chloroflexi, and Bacteroidetes) were present in all blade surface samples. This study provides new insights and understanding of the processes that influence the structure of marine phyllosphere communities, how these microbial communities relate to their host, and their role as a part of the seagrass holobiont, which is an important contribution given the current decline of seagrass coverage worldwide.

Distinct Microbial Community of Phyllosphere Associated with Five Tropical Plants on Yongxing Island, South China Sea

The surfaces of a leaf are unique and wide habitats for a microbial community. These microorganisms play a key role in plant growth and adaptation to adverse conditions, such as producing growth factors to promote plant growth and inhibiting pathogens to protect host plants. The composition of microbial communities very greatly amongst different plant species, yet there is little data on the composition of the microbiome of the host plants on the coral island in the South China Sea. In this study, we investigated the abundances and members of a major microbial community (fungi, bacteria, and diazotrophs) on the leaves of five dominant plant species (Ipomoea pes-caprae, Wedelia chinensis, Scaevola sericea, Cocos nucifera, and Sesuvium portulacastrum) on the island using real-time quantitative polymerase chain reaction (PCR) and high-throughput amplicon sequencing. Quantitative PCR results showed that fungi and bacteria were ubiquitous and variable among different host plants. Scaevola sericea showed the lowest absolute abundance and highest diversity of fungi and bacteria, while Cocos nucifera had the lowest abundance and the highest diversity of diazotrophs compare to the other four plants. There was a small proportion of shared microorganisms among the five different plants, while unique fungi, bacteria and diazotrophs were significantly enriched for different host plant species in this study (p < 0.05). Some of the most abundant organisms found in the communities of these different host plants are involved in important biogeochemical cycles that can benefit their host, including carbon and nitrogen cycles.

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.