Effects of nutrient loading on sediment bacterial and pathogen communities within seagrass meadows

Spatio-temporal structuring and assembly of abundant and rare bacteria in the benthic compartment of a marginally eutrophic lagoon

The investigations on ecological processes that structure abundant and rare sub-communities are limited from the benthic compartments of tropical brackish lagoons. We examined the spatial and temporal patterns in benthic bacterial communities of a brackish lagoon; Chilika. Abundant and rare bacteria showed differences in niche specialization but exhibited similar distance-decay patterns. Abundant bacteria were mostly habitat generalists due to their broader niche breadth, environmental response thresholds, and greater functional redundancy. In contrast, rare bacteria were mostly habitat specialists due to their narrow niche breadth, lower environmental response thresholds, and functional redundancy. The spatial patterns in abundant bacteria were largely shaped by stochastic processes (88.7 %, mostly dispersal limitation). In contrast, rare bacteria were mostly structured by deterministic processes (56.4 %, mostly heterogeneous selection). These findings provided a quantitative assessment of the different forces namely spatial, environmental, and biotic that together structured bacterial communities in the benthic compartment of a marginally eutrophic lagoon.

Spatio-temporal variation of bacterial community structure in two intertidal sediment types of Jiaozhou Bay

The intertidal sediment environment is dynamic and the biofilm bacterial community within it must constantly adapt, but an understanding of the differences in the biofilm bacterial community within sediments of different types is still relatively limited. The semi-enclosed Jiaozhou Bay has a temperate monsoon climate, with strong currents at the mouth of the bay. In this study, the structure of the bacterial community in Jiaozhou Bay sediment biofilms are described using high-throughput 16 S rRNA gene sequencing and the effects of temporal change and different sediment environment types are discussed. Alpha diversity was significantly higher in sandy samples than in muddy samples. Sandy sediments with increased heterogeneity promote bacterial aggregation. Beta diversity analysis showed significant differences between sediment types and between stations. Proteobacteria and Acidobacteria were significantly more abundant at ZQ, while Campilobacterota was significantly more abundant at LC. The relative abundances of Bacteroidetes, Campilobacterota, Firmicutes, and Chloroflexi were significantly higher in the muddy samples, while Actinobacteria and Proteobacteria were higher in the sandy samples. There were different phylum-level biomarkers between sediment types at different stations. There were also different patterns of functional enrichment in biogeochemical cycles between sediment types and stations with the former having more gene families that differed significantly, highlighting their greater role in determining bacterial function. Bacterial amplicon sequence variant variation between months was less than KEGG ortholog variation between months, presumably the temporal change had an impact on shaping the intertidal sediment bacterial community, although this was less clear at the gene family level. Random forest prediction yielded a combination of 43 family-level features that responded well to temporal change, reflecting the influence of temporal change on sediment biofilm bacteria.

Leptospirosis and the Environment: A Review and Future Directions

Leptospirosis is a zoonotic disease of global importance with significant morbidity and mortality. However, the disease is frequently overlooked and underdiagnosed, leading to uncertainty of the true scale and severity of the disease. A neglected tropical disease, leptospirosis disproportionately impacts disadvantaged socioeconomic communities most vulnerable to outbreaks of zoonotic disease, due to contact with infectious animals and contaminated soils and waters. With growing evidence that Leptospira survives, persists, and reproduces in the environment, this paper reviews the current understanding of the pathogen in the environment and highlights the unknowns that are most important for future study. Through a systematic Boolean review of the literature, our study finds that detailed field-based study of Leptospira prevalence, survival, and transmission in natural waters and soils is lacking from the current literature. This review identified a strong need for assessment of physical characteristics and biogeochemical processes that support long-term viability of Leptospira in the environment followed by epidemiological assessment of the transmission and movement of the same strains of Leptospira in the present wildlife and livestock as the first steps in improving our understanding of the environmental stage of the leptospirosis transmission cycle.

Nutrient loading decreases blue carbon by mediating fungi activities within seagrass meadows

Coastal pollution, including nutrient loading, can negatively impact seagrass health and cover and may consequently alter soil organic carbon (SOC) accumulation and preservation. Key to understanding how eutrophication impacts SOC cycling in seagrass ecosystems is how nutrient loading changes the sources of carbon being deposited and how these changes in resources, both nutrients and carbon availability, influence soil microbiota community and activity. Currently, the direction and magnitude of nutrient loading impacts on seagrass SOC dynamics are poorly understood at a meadow scale, limiting our ability to reveal the driving mechanisms of SOC remineralisation. The purpose of this study was to assess the response of surface SOC and soil microbiomes to nutrient loading within tropical seagrass meadows. To achieve this, we quantified both total SOC and recalcitrant soil organic carbon (RSOC) concentrations and sources, in addition to the composition of bacterial and fungal communities and soil extracellular enzyme activities. We found that nutrient loading elevated SOC and RSOC content, mainly facilitated by enhanced algal growth. There was no nutrient effect on the soil prokaryotic communities, however, saprotrophic fungi groups (i.e. Trapeliales, Sordaridales, Saccharomycetales and Polyporales) and fungal activities were elevated under high nutrient conditions, including extracellular enzyme activities linked to seagrass-based cellulose and lignin decomposition. This relative increase in RSOC transformation may decrease the relative contribution of seagrass carbon to RSOC pools. Additionally, significantly different fungal communities were observed between adjacent T. hemprichii and E. acoroides areas, which coincided with elevated RSOC-decomposing enzyme activity in T. hemprichii meadows, even though the mixed seagrass meadow received allochthonous SOC and RSOC from the same sources. These results suggest that nutrient loading stimulated fungal activity and community shifts specific to the local seagrass species, thereby causing fine-scale (within-meadow) variability in SOC cycling in response to nutrient loading. This study provides evidence that fungal composition and activity, mediated by human activities (e.g. nutrient loading), can be an important influence on seagrass blue carbon accumulation and remineralisation.

Mapping and Spatial Variation of Seagrasses in Xincun, Hainan Province, China, Based on Satellite Images

Seagrass is an important structural and functional component of the global marine ecosystem and is of high value for its ecological services. This paper took Xincun Bay (including Xincun Harbor and Li’an Harbor) of Hainan Province as the study area, combined ground truth data, and adopted two methods to map seagrass in 2020 using Chinese GF2 satellite images: maximum-likelihood and object-oriented classification. Sentinel-2 images from 2016 to 2020 were used to extract information on seagrass distribution changes. The following conclusions were obtained. (1) Based on GF2 imagery, both the classical maximum likelihood classification (MLC) method and the object-based image analysis (OBIA) method can effectively extract seagrass information, and OBIA can also portray the overall condition of seagrass patches. (2) The total seagrass area in the study area in 2020 was about 395 hectares, most of which was distributed in Xincun Harbor. The southern coast of Xincun Harbor is an important area where seagrass is concentrated over about 228 hectares in a strip-like continuous distribution along the coastline. (3) The distribution of seagrasses in the study area showed a significant decaying trend from 2016 to 2020. The total area of seagrass decreased by 79.224 ha during the five years from 2016 to 2020, with a decay rate of 16.458%. This study is the first on the comprehensive monitoring of seagrass in Xincun Bay using satellite remote sensing images, and comprises the first use of GF2 data in seagrass research, aiming to provide a reference for remote sensing monitoring of seagrass in the South China Sea.

Tracking the impacts of nutrient inputs on estuary ecosystem function

Estuaries are one of the most impacted coastal environments globally, subjected to multiple stressors from urban, industry and coastal development. With increasing anthropogenic activity surrounding estuarine systems, sewage inputs have become a common concern. Stable isotope analysis provides a well-established tool to investigate the incorporation of nitrogen into marine organisms and identify major nutrient sources. Benthic macroinvertebrate communities are often used as bioindicators in ecological studies as they typically display predictable responses to anthropogenic pressures, however have a suite of limitations and costs associated with their use. 16S rDNA amplicon sequencing techniques allow for investigation of the microbial communities inhabiting complex environmental samples, with potential as a tool in the ecological assessment of pollution. These communities have not yet been adequately considered for ecological studies and biomonitoring, with a need to better understand interactions with environmental stressors and implications for ecosystem function. This study used a combination of stable isotope analysis to trace the uptake of anthropogenic nitrogen in biota, traditional assessment of benthic macroinvertebrate communities, and 16S rDNA genotyping of benthic microbial communities. Stable isotope analysis of seagrass and epiphytes identified multiple treated and untreated sewage inputs, ranges of 5.2-7.2‰ and 1.9-4.0‰ for δ¹⁵N respectively, as the dominant nitrogen source at specific locations. The benthic macroinvertebrate community reflected these inputs with shifts in dominant taxa and high abundances of polychaetes at some sites. Microbial communities provided a sensitive indication of impact with a breadth of information not available using traditional techniques. Composition and predicted function reflected sewage inputs, particularly within sediments, with the relative abundance of specific taxa and putative pathogens linked to these inputs. This research supports the growing body of evidence that benthic microbial communities respond rapidly to anthropogenic stressors and have potential as a monitoring tool in urban estuarine systems.

Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds

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

Infective prey leads to a partial role reversal in a predator-prey interaction

An infective prey has the potential to infect, kill and consume its predator. Such a prey-predator relationship fundamentally differs from the predator-prey interaction because the prey can directly profit from the predator as a growth resource. Here we present a population dynamics model of partial role reversal in the predator-prey interaction of two species, the bottom dwelling marine deposit feeder sea cucumber Apostichopus japonicus and an important food source for the sea cucumber but potentially infective bacterium Vibrio splendidus. We analyse the effects of different parameters, e.g. infectivity and grazing rate, on the population sizes. We show that relative population sizes of the sea cucumber and V. Splendidus may switch with increasing infectivity. We also show that in the partial role reversal interaction the infective prey may benefit from the presence of the predator such that the population size may exceed the value of the carrying capacity of the prey in the absence of the predator. We also analysed the conditions for species extinction. The extinction of the prey, V. splendidus, may occur when its growth rate is low, or in the absence of infectivity. The extinction of the predator, A. japonicus, may follow if either the infectivity of the prey is high or a moderately infective prey is abundant. We conclude that partial role reversal is an undervalued subject in predator-prey studies.

Manure derived nutrients alter microbial community composition and increase the presence of potential pathogens in freshwater sediment

AIM

To determine the impact of an acute, pulse disturbance of nutrients from manure on freshwater sediment microbiomes in an experimental system.

METHODS AND RESULTS

A controlled freshwater mesocosm experiment was designed to compare the effect of disturbance from nutrients derived from sterile manure (SM), disturbance from equivalent concentrations of laboratory-derived nutrients, and a nondisturbed control on freshwater sediment microbial community composition and function using 16S rRNA amplicon sequencing. Sediment microbiomes impacted by nutrients from SM showed no sign of compositional recovery after 28 days but those impacted by laboratory-derived chemicals lead to a new steady-state (p < 0.05). Carbon and nitrate sources within disturbed mesocosms were the primary drivers of altered microbial community composition. Additionally, multiple potential pathogens (based on exact sequence matching at the species level) were enriched in mesocosms treated with SM.

CONCLUSIONS

Nutrient disturbance from SM, in the absence of the manure microbial community, alters the microbiome of sediments without recovery after 28 days and enriches potential pathogens.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results suggest manure land application practices should be re-evaluated to account for impact of nutrient disturbance on environmental microbiomes in addition to the impact of the manure microbial community.

What drives putative bacterial pathogens removal within seagrass meadows?

To analyze the mechanism of bacterial pathogen removal in seagrass meadows, we compared bacterial pathogens abundance in trapped particles in different seagrass meadows under different intensities of human activities. We compared the particle deposition rates and abundances of bacterial pathogen in Thalassia hemprichii, Enhalus acoroides stands and adjacent unvegetated patches. The bacterial pathogens abundance was much higher in E. acoroides than in adjacent unvegetated patches, however, the trapped particles under T. hemprichii were lower than in nearby unvegetated areas with the exception of the pristine seagrass meadow. These results indicate that seagrass, at least E. acoroides, can remove bacterial pathogens by trapping particles. What is unknown, nevertheless, is how the trapped bacterial pathogens are removed by T. hemprichii. We put forward that antibacterial chemical compounds release from seagrass was stimulated by stress from human activities for inhibition of bacterial pathogen. This putative mechanism needs to be explored in future studies.

Rhizosphere microbiome dynamics in tropical seagrass under short-term inorganic nitrogen fertilization

Rhizosphere microbes are crucial to seagrass meadows because they promote plant growth and heath. However, information concerning the response of rhizosphere microorganisms in seagrass sediment in the presence of different nitrogen sources is lacking. Here, by means of high-throughput sequencing, we investigated how addition of inorganic nitrogen affects the rhizosphere microbiome of the tropical seagrass Thalassia hemperichii. A seagrass culture system was set up to conduct a nitrogen addition (ammonium and nitrate) simulation experiment. We found that the relative abundance of Proteobacteria and Bacteroidetes was increased in inorganic nitrogen-enriched samples, whereas that of Acidobacteria decreased under ammonium enrichment, especially after 35 days. High levels of inorganic nitrogen addition caused a significant decrease in the relative abundance of Desulfobacteraceae, Sulfurovaceae, and Spirochaetes, which are primarily involved in sulfur cycling. Additionally, the abundance of microbes in the seagrass rhizosphere reached the highest after the ammonium-enrichment treatment. Among the analyzed seagrass photosynthetic characteristics, seagrass leaves presented the highest light utility in treatments receiving nitrate, followed by the control groups and ammonium-enrichment groups. Moreover, 16S rRNA gene-predicted functional analysis suggested that some functions related to metabolism of amino acids and signal transduction were enriched in samples receiving high ammonium, whereas nitrate addition enriched predicted functions related to diseases. These findings provide new insights into the response of microbial communities to different types of nitrogen additions in seagrass ecosystems.

Nutrient enrichment increases size of Zostera marina shoots and enriches for sulfur and nitrogen cycling bacteria in root-associated microbiomes

Seagrasses are vital coastal ecosystem engineers, which are mutualistically associated with microbial communities that contribute to the ecosystem services provided by meadows. The seagrass microbiome and sediment microbiota play vital roles in belowground biogeochemical and carbon cycling. These activities are influenced by nutrient, carbon and oxygen availability, all of which are modulated by environmental factors and plant physiology. Seagrass meadows are increasingly threatened by nutrient pollution, and it is unknown how the seagrass microbiome will respond to this stressor. We investigated the effects of fertilization on the physiology, morphology and microbiome of eelgrass (Zostera marina) cultivated over 4 weeks in mesocosms. We analyzed the community structure associated with eelgrass leaf, root and rhizosphere microbiomes, and of communities from water column and bulk sediment using 16S rRNA amplicon sequencing. Fertilization led to a higher number of leaves compared with that of eelgrass kept under ambient conditions. Additionally, fertilization led to enrichment of sulfur and nitrogen bacteria in belowground communities. These results suggest nutrient enrichment can stimulate belowground biogeochemical cycling, potentially exacerbating sulfide toxicity in sediments and decreasing future carbon sequestration stocks.

Seagrass vegetation affect the vertical organization of microbial communities in sediment

Seagrasses represent high primary productivity and provide important ecosystem services to the marine environment. Seagrass-associated microbial communities are playing essential ecological functional roles in biogeochemical cycles. However, little is known about the effect of seagrass vegetation on microbial communities in sediment. In the present study, the sediment cores of seagrass bed (dominated by Zostera japonica and Zostera marine) and degradation area in Swan Lake (China) were sampled; then, biogeochemical parameters were analyzed, and microbial community composition was investigated by using high-throughput sequencing of the 16S rRNA gene. The results showed that the presence of seagrass could lead to a decrease in the richness and diversity of the microbial community. In the vertical direction, a pronounced shift from Proteobacteria-dominated upper layers to Chloroflexi and Crenarchaeota-dominated deep layers in all sediment cores were observed. Besides, Bathyarchaeia is more abundant at degradation area, while Vibrionaceae, Sulfurovum and Lokiarchaeial overrepresent at the seagrass bed area. Vibrionaceae was abundant in the rhizosphere of Z. marina and Z. japonica, and the proportions reached 84.45% and 63.89%, respectively. This enrichment of Vibrio spp. may be caused by the macrobenthic species near the seagrass rhizosphere, and these Vibrio spp. reduced the diversity and stability of microbial community, which may lead to the degradation of seagrass. This study would provide clues for the distribution patterns and niche preferences of seagrass microbiome. The conservation strategy of seagrass would be further elucidated from the perspective of the microbiome.

Coupled changes of bacterial community and function in the gut of mud crab (Scylla Paramamosain) in response to Baimang disease

Increasing evidence has revealed a close association between intestinal bacterial community and hosts health. However, it is unclear whether and what extend Baimang disease alters the intestinal microbiota in mud crab (Scylla paramamosain). Here, we conducted intestinal contents Illumina sequencing of healthy and Baimang diseased mud crab (S. paramamosain) to understand bacterial community variations among health status. In addition, bacterial functional predication was used to investigate whether and how the bacteria variations further change their functions? The phyla of Proteobacteria, Fusobacteria, Cyanobacteria, Tenericutes, Firmicutes, Bacteroidetes, and Spirochaetae constituted over 96.44% of the total intestinal bacteria, with being the dominant taxa. The 7 most significantly different orders, including the increased four orders of Clostridiales, Entomoplasmatales, Bacteroidales, and Mycoplasmatales and the decreased three orders of Vibrionales, Campylobacterales, and Fusobacteriales, accounted for 61.14% dissimilarity, probably being the indicator taxa of Baimang disease. Accordingly, 12 Kyoto Encyclopedia of Genes and Genomes orthologies in level 3 shifted significantly at the diseased crabs. Especially, bacterial secretion system, secretion system, lipopolysaccharide biosynthesis proteins and Vibrio cholerae pathogenic cycle, being related to bacterial virulence, were reduced. In addition, the reduced butanoate metabolism, and induced methane metabolism and one carbon pool by folate were important metabolic processes of probiotic, such as Bacteroides spp. and Clostridium spp., with playing critical roles in host health. This study suggests that Baimang disease coupled altered the intestinal bacterial communities and functions, providing timely information for further analysis the influencing mechanism of Baimang disease in mud crab (S. paramamosain).

Seaweed Loads Cause Stronger Bacterial Community Shifts in Coastal Lagoon Sediments Than Nutrient Loads

The input of nutrients from anthropogenic sources is the leading cause of coastal eutrophication and is usually coupled with algal/seaweed blooms. Effects may be magnified in semi-enclosed systems, such as highly productive coastal lagoon ecosystems. Eutrophication and seaweed blooms can lead to ecosystem disruption. Previous studies have considered only one of these factors, disregarding possible interactive effects and the effect of the blooming species' identity on sediment bacterial communities. We tested the effect of experimental nutrient loading and two common blooming seaweeds (Ulva rigida and Gracilaria vermiculophylla) in coastal lagoon sediments, on the structure of bacterial communities (using 16S rRNA amplicon sequencing) and corresponding putative functional potential (using PiCRUSt). At the Operational Taxonomic Unit (OTU) level, the addition of nutrients reduced bacterial community α-diversity and decreased the abundance of sulfate reducers (Desulfobacterales) compared to sulfur oxidizers/denitrifiers (Chromatiales and Campylobacterales), whereas this was not the case at the order level. Seaweed addition did not change bacterial α-diversity and the effect on community structure depended on the taxonomic level considered. The addition of Gracilaria increased the abundance of orders and OTUs involved in sulfate reduction and organic matter decomposition (Desulfobacterales, Bacteroidales, and Clostridiales, respectively), an effect which was also detected when only Ulva was added. Nutrients and the seaweeds combined only interacted for Ulva and nutrients, which increased known sulfide oxidizers and denitrifiers (order Campylobacterales). Seaweed enrichment affected putative functional profiles; a stronger increase of sulfur cycling KEGG pathways was assigned to nutrient-disturbed sediments, particularly with the seaweeds and especially Ulva. In contrast, nitrogen and sulfur cycle pathways showed a higher abundance of genes related to dissimilatory nitrate reduction to ammonium (DNRA) in Ulva+nutrients treatments. However, the other seaweed treatments increased the nitrogen fixation genes. Thiosulfate reduction, performed by sulfate-reducing bacteria, increased in seaweed treatments except when Ulva was combined with nutrients. In conclusion, the in situ addition of nutrients and the seaweeds to intertidal sediments affected the bacterial communities differently and independently. The predicted functional profile suggests a shift in relative abundances of putative pathways for nitrogen and sulfur cycles, in line with the taxonomic changes of the bacterial communities.

Effects of nutrient loading on sediment bacterial and pathogen communities within seagrass meadows

Eutrophication can play a significant role in seagrass decline and habitat loss. Microorganisms in seagrass sediments are essential to many important ecosystem processes, including nutrient cycling and seagrass ecosystem health. However, current knowledge of the bacterial communities, both beneficial and detrimental, within seagrass meadows in response to nutrient loading is limited. We studied the response of sediment bacterial and pathogen communities to nutrient enrichment on a tropical seagrass meadow in Xincun Bay, South China Sea. The bacterial taxonomic groups across all sites were dominated by the Gammaproteobacteria and Firmicutes. Sites nearest to the nutrient source and with the highest NH₄⁺ and PO₄³⁻ content had approximately double the relative abundance of putative denitrifiers Vibrionales, Alteromonadales, and Pseudomonadales. Additionally, the relative abundance of potential pathogen groups, especially Vibrio spp. and Pseudoalteromonas spp., was approximately 2‐fold greater at the sites with the highest nutrient loads compared to sites further from the source. These results suggest that proximity to sources of nutrient pollution increases the occurrence of potential bacterial pathogens that could affect fishes, invertebrates and humans. This study shows that nutrient enrichment does elicit shifts in bacterial community diversity and likely their function in local biogeochemical cycling and as a potential source of infectious diseases within seagrass meadows.