Environmental drivers affecting the bacterial community of intertidal sediments in the Yellow Sea

Occurrence, Source Apportionment, and Risk Assessment of Antibiotics in Mangrove Sediments from the Lianzhou Bay, China

In recent years, the widespread application of antibiotics has raised global concerns, posing a severe threat to ecological health. In this study, the occurrence, source, and ecological risks of 39 antibiotics belonging to 5 classes in mangrove sediments from Lianzhou Bay, China, were assessed. The total concentrations of the antibiotics (∑39 antibiotics) ranged from 65.45 to 202.24 ng/g dry weight (dw), with an average of 142.73 ± 36.76 ng/g dw. The concentrations of these five classes of antibiotics were as follows: Sulfonamides (SAs) > Tetracyclines (TCs) > Fluoroquinolones (QUs) > Penicillin (PCs) > Macrolides (MLs). The spatial distribution of antibiotics varied as high tidal zone > middle tidal zone > low tidal zone. The total organic carbon (TOC), pH, nitrate (NO3--N), and nitrite (NO2--N) of the sediment significantly influenced the distribution of antibiotics (p < 0.05). A source analysis identified untreated sewage from aquaculture as the primary source of antibiotics in the local mangrove. A risk assessment revealed that ciprofloxacin, norfloxacin, ofloxacin of QUs, and tetracycline of TCs exhibited medium risks to algae in certain sampling sites, while other antibiotics exhibited low or no risks to all organisms. Nevertheless, the total risk of all the detected antibiotics to algae was medium in 95% of the sites. The overall ecological risk level of antibiotics in the middle tidal zone was slightly lower than in the high tidal zone and the lowest in the low tidal zone. In summary, the experimental results provided insights into the fate and transport behaviors of antibiotics in mangrove sediments from Lianzhou Bay.

Heavy metals in a typical industrial area-groundwater system: Spatial distribution, microbial response and ecological risk

The environmental burden due to industrial activities has been quite observable in the last few years, with heavy metals (HMs) like lead, cadmium, and arsenic inducing serious perturbations to the microbial ecosystem of groundwater. Studies carried out in North China, a region known for interconnection of industrial and groundwater systems, sought to explore the natural mechanisms of adaptation of microbes to groundwater contamination. The results showed that heavy metals permeate from surface increased the diversity and abundance of microbial communities in groundwater, producing an average decrease of 40.84% and 34.62% in the relative abundance of Bacteroidetes and Proteobacteria in groundwater, respectively. Meanwhile, the key environmental factors driving the evolution of microbial communities shift from groundwater nutrients to heavy metals, which explained 50.80% of the change in the microbial community composition. Microbial indicators are more sensitive to HMs pollution and could accurately identify industrial area where HMs permeation occurred and other extraneous pollutants. The phylum Bacteroidetes could act as appropriate indicators for the identification. Significant genera that were identified, being Mesorhizobium, Clostridium, Bacillus and Mucilaginibacter, were found to play important roles in the microbial network in terms of the potential to assist in groundwater clean-up. Notably, pollution from heavy metals has diminished the effectiveness and resilience of microbial communities in groundwater, thereby heightening the susceptibility of these normally stable microbial ecosystems. These findings offer new perspectives on how to monitor and detect groundwater pollution, and provide scientific guidance for developing suitable remediation methods for groundwater contaminated with heavy metals. Future research is essential explore the application of metal-tolerant or resistant bacteria in bioremediation strategies to rehabilitate groundwater systems contaminated by HMs.

Metals and microorganisms in a Maar lake sediment core indicating the anthropogenic impact over last 800 years

A closed Maar lake, receiving mostly atmospheric deposition, offers a unique setting for investigating the impact of human activities on the environment. In this study, we aimed to investigate the historical record of metals in core sediments of Maar Lake in Huguangyan (HGY), Southeast China, and elucidate the possible microbial responses to anthropogenic metal stress. Five stages were divided according to the historical record of metals and corresponding distribution of microbial community, among which Pb and Sn showed a peak value around 1760 CE, indicating the ancient mining and smelting activities. Since the 1980s, a substantial enrichment of metals such as Zn, As, Mo, Cd, Sn, Sb, and Pb was observed, due to the rapid industrial growth in China. In terms of microorganisms, Chloroflexi phylum, particularly dominated by Anaerolineales, showed significant correlations with Pb and Sn, and could potentially serve as indicator species for mining and smelting-related contamination. Desulfarculales and Desulfobacterales were found to be more prevalent in recent period and exhibited positive correlations with anthropogenic metals. Moreover, according to the multivariate regression modeling and variance decomposition analysis, Pb and Sn could regulate Anaerolineales and further pose impact on the carbon cycle; while sulfate-reducing bacteria (SRB) could response to anthropogenic metals and influence sulfur cycle. These findings provide new insights into the interaction between metals and microbial communities over human history.

Composition of Particulate Matter and Bacterial Community in Gut Contents and Surrounding Sediments of Three Sipunculan Species (Siphonosoma australe, Phascolosoma arcuatum, and Sipunculus nudus)

Siphonosoma australe, Phascolosoma arcuatum, and Sipunculus nudus are three important sipunculan species in tropical intertidal zones. In this study, the particle size, organic matter content, and bacterial community composition in the gut contents of three different sipunculans and their surrounding sediments were analyzed. The grain size fractions of sipunculans' guts were significantly different from those of their surrounding sediments; particle size fractions < 500 μm were favored by the sipunculans. As for the total organic matter (TOM), higher contents of organic matter were observed in the guts than in the surrounding sediments in all three sipunculan species. The bacterial community composition of all the samples was investigated by 16S rRNA gene sequencing, in which a total of 8974 OTUs were obtained from 24 samples based on a 97% threshold. The predominant phylum identified from the gut contents of three sipunculans was Planctomycetota, while the predominant phylum in their surrounding sediments was Proteobacteria. At the genus level, the most abundant genus was Sulfurovum (average 4.36%) in the surrounding sediments, while the most abundant genus was Gplla (average 12.76%) in the gut contents. The UPGMA tree showed that the samples from the guts of three different sipunculans and their surrounding sediments were clustered separately into two groups, which showed that these three sipunculans had a different bacterial community composition with their surrounding sediments. The grain size and total organic matter (TOM) had the greatest impacts on the bacterial community composition at both the phylum and genus levels. In conclusion, the differences in particle size fractions, organic matter content, and bacterial community composition between the gut contents and surrounding sediments in these three sipunculan species might be caused by their selective ingestion.

PhyloPlus: a Universal Tool for Phylogenetic Interrogation of Metagenomic Communities

Phylogeny is a powerful tool that can be incorporated into quantitative descriptions of community diversity, yet its use has been limited largely due to the difficulty in constructing phylogenies which incorporate the wide genomic diversity of microbial communities. Here, we describe the development of a web portal, PhyloPlus, which enables users to generate customized phylogenies that may be applied to any bacterial or archaeal communities. We demonstrate the power of phylogeny by comparing metrics that employ phylogeny with those that do not when applied to data sets from two metagenomic studies (fermented food, n = 58; human microbiome, n = 60). This example shows how inclusion of all bacterial species identified by taxonomic classifiers (Kraken2 and Kaiju) made the phylogeny perfectly congruent to the corresponding classification outputs. Our phylogeny-based approach also enabled the construction of more constrained null models which (i) shed light into community structure and (ii) minimize potential inflation of type I errors. Construction of such null models allowed for the observation of under-dispersion in 44 (75.86%) food samples, with the metacommunity defined as bacteria that were found in different food matrices. We also observed that closely related species with high abundance and uneven distribution across different sites could potentially exaggerate the dissimilarity between phylogenetically similar communities if they were measured using traditional species-based metrics (P_adj. = 0.003), whereas this effect was mitigated by incorporating phylogeny (P_adj. = 1). In summary, our tool can provide additional insights into microbial communities of interest and facilitate the use of phylogeny-based approaches in metagenomic analyses. IMPORTANCE There has been an explosion of interest in how microbial diversity affects human health, food safety, and environmental functions among many other processes. Accurately measuring the diversity and structure of those communities is central to understanding their effects. Here, we describe the development of a freely available online tool, PhyloPlus, which allows users to generate custom phylogenies that may be applied to any data set, thereby removing a major obstacle to the application of phylogeny to metagenomic data analysis. We demonstrate that the genetic relatedness of the organisms within those communities is a critical feature of their overall diversity, and that using a phylogeny which captures and quantifies this diversity allows for much more accurate descriptions while preventing misleading conclusions based on estimates that ignore evolutionary relationships.

Effects of Salinity on Assembly Characteristics and Function of Microbial Communities in the Phyllosphere and Rhizosphere of Salt-Tolerant Avicennia marina Mangrove Species

It is of great significance to explore the structure and salinity response of microbial communities in salt-tolerant plants to understand the mechanisms of plant-microbe interactions. Herein, we investigated the phyllosphere and rhizosphere microbial communities of Avicennia marina, a pioneer salt-tolerant plant, at three sites with different salinities in the coastal intertidal zone. The results showed that salinity had different effects on phyllosphere and rhizosphere microbial communities and had a greater impact on bacterial communities and bacterial network interactions. The rhizosphere bacterial community alpha diversity significantly increased with increasing salinity. Moreover, the relative abundance of Proteobacteria decreased significantly, while that of Bacteroidota and Actinobacteriota, with stronger salt tolerance and nutrient utilization capacity, increased significantly. Functional prediction indicated that the microbial communities could produce catalase, peroxidase, 3-phytase, and tryptophan synthase, which may exert potential antistress and growth-promoting functions. Among them, catalase, 3-phytase, alkaline phosphatase, and acid phosphatase increased significantly in the phyllosphere and rhizosphere bacterial communities and the phyllosphere fungal community with increasing salinity. Importantly, the dominant taxa Kushneria and Bacillus, which are salt tolerant and growth promoting, were isolated from the phyllosphere and rhizosphere, respectively, and verified to have the ability to alleviate salt stress and promote the growth of rice. IMPORTANCE Avicennia marina is a pioneer salt-tolerant plant in coastal intertidal mangroves, an efficient blue carbon ecosystem. It is of great importance to explore how salinity affects the phyllosphere and rhizosphere microbial communities of A. marina. This study showed that the microbial communities in the phyllosphere and rhizosphere of A. marina had different constitutive properties, adaptive network interactions, and potential stress-promoting functions. Furthermore, the dominant bacteria Kushneria and Bacillus were obtained from the phyllosphere and rhizosphere, respectively, and their coculture with rice could effectively alleviate salt stress and promote rice growth. Additionally, the effects of salinity changes on microbial community structure, associations, and functional potential in the phyllosphere and rhizosphere of A. marina were observed. This study has enriched our understanding of the microbial community structure, function, and ecological stability of mangrove species in coastal intertidal zones and has practical significance for improving crop yield by using salt-tolerant plant microbiomes.

Evidence that offshore wind farms might affect marine sediment quality and microbial communities

Offshore wind power is a typical example of clean energy production and plays a critical role in achieving carbon neutrality. Offshore wind farms can have an impact on the marine environment, especially sedimentary environments, but their influence on sediments remain largely unknown. This study, which uses the control-impact principle to define different areas, investigated the characteristics of marine sediments under the Putidao offshore wind farm in Bohai Bay, China. We used chemical and microbiological observations to evaluate sediment quality and microbial community structure. According to both the geo-accumulation index (I_geo) and contamination factor (CF) indexes, copper, chromium and zinc were the major contaminants in the offshore wind farm sediments. The pollution load index (PLI) index showed that the various sites on the wind farm were only lightly polluted compared with baseline values. Closer to the wind farm's center, the metal concentrations started to rise. The physicochemical features of the sediments could better explain changes in the microorganisms present, and screening the microbiomes showed a correlation with heavy metal levels, linking the relative abundance of microorganisms to the sediment quality index. This comprehensive study fills a knowledge gap in China and adds to our understanding of how to assess the sedimentary environments of offshore wind farms.

Response mechanism of microorganisms to the inhibition of endogenous pollution release by calcium peroxide

To further explore the response mechanism of microorganisms to the synchronous control of nitrogen and phosphorus release from sediments by CaO₂, the spatiotemporal changes in the physical, chemical and biological indicators of the overlying water, interstitial water and sediments in each reactor were measured in the experiment. The experiment results showed that CaO₂ could increase the ammonia monooxygenase activity, nitrite oxidase activity and Nitrospira abundance in the sediment near its dosing position, and enhanced the activities of nitrate reductase and nitrite reductase at a certain distance from the dosing position, thereby promoting nitrogen removal in sediments through the alternating process of nitrification and denitrification. At the same time, the increase of alkaline phosphatase activity and Saccharimonadales abundance in the test groups accelerated the hydrolysis of organic phosphorus, and the P immobilization in sediments was realized through the subsequent precipitation reaction of Ca²⁺ and PO₄^3- under alkaline conditions. In addition, the enhanced activities of dehydrogenase and catalase ensured that CaO₂ would not cause great killing effect on microorganisms when improving the hypoxic conditions and inhibiting endogenous release. As a result, the dissolved product of CaO₂ such as Ca(OH)₂ and H₂O₂ reduced the nutrients concentration and killed the algae, which kept the algae density and chlorophyll a concentration at a low level throughout the test groups. Therefore, this study systematically clarified the microbial mechanism of CaO₂ synchronously controlling the release of nitrogen and phosphorus from sediments, which provided a new idea for the remediation of endogenous pollution in the water system.

Effects of emerging contaminants and heavy metals on variation in bacterial communities in estuarine sediments

Emerging contaminants (ECs) and heavy metals (HMs) are universally present together in estuarine sediments; despite this, their effects on microbial communities have been widely studied separately, rather than in consort. In this study, the combined effects of ECs and HMs on microbial communities were investigated in sediments from 11 major river estuaries around the Bohai Sea, China. Proteobacteria, Bacteroidetes, and Firmicutes were the dominant phyla in the sediments. Using Shannon indices, total phosphorus and total organic carbon were shown to affect microbial community structure. Redundancy analysis of microbial variation implicated Cd and As as the greatest pollutants, followed by Mn, Fe, Zn and Cu; no impacts from galaxolide (HHCB) and tonalide (AHTN) were found. Correlation analysis demonstrated that the concentration of ECs increased the abundance of certain bacteria (e.g., Haliangium, Altererythrobacter, Gaiella and Erythrobacter), and therefore these can be used as potential contamination indicators. Shannon indices and Chao1 indices showed that there were differences in the richness and diversity of bacterial communities in the sediments of 11 rivers. The principal coordinate analysis displayed higher similarity of bacterial community composition in estuarine sediments in Liaoning province than other regions. The results can be used to predict changes in estuary ecosystems to maintain their ecological balance and health.

Functional and Seasonal Changes in the Structure of Microbiome Inhabiting Bottom Sediments of a Pond Intended for Ecological King Carp Farming

Simple Summary

Bottom sediments are usually classified as extreme habitats for microorganisms. They are defined as matter deposited on the bottom of water bodies through the sedimentation process. The quality of sediments is extremely important for the good environmental status of water, because they are an integral part of the surface water environment. Microorganisms living in sediments are involved in biogeochemical transformations and play a fundamental role in maintaining water purity, decomposition of organic matter, and primary production. As a rule, studies on bottom sediments focus on monitoring their chemistry and pollution, while little is known about the structure of bacterial communities inhabiting this extreme environment. In this study, Next-Generation Sequencing (NGS) was combined with the Community-Level Physiological Profiling (CLPP) technique to obtain a holistic picture of bacterial biodiversity in the bottom sediments from Cardinal Pond intended for ecological king carp farming. It was evident that the bottom sediments of the studied pond were characterized by a rich microbiota composition, whose structure and activity depended on the season, and the most extensive modifications of the biodiversity and functionality of microorganisms were noted in summer.

Abstract

The main goal of the study was to determine changes in the bacterial structure in bottom sediments occurring over the seasons of the year and to estimate microbial metabolic activity. Bottom sediments were collected four times in the year (spring, summer, autumn, and winter) from 10 different measurement points in Cardinal Pond (Ślesin, NW Poland). The Next-Generation Sequencing (MiSeq Illumina) and Community-Level Physiological Profiling techniques were used for identification of the bacterial diversity structure and bacterial metabolic and functional activities over the four seasons. It was evident that Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant phyla, while representatives of Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria predominated at the class level in the bottom sediments. An impact of the season on biodiversity and metabolic activity was revealed with the emphasis that the environmental conditions in summer modified the studied parameters most strongly. Carboxylic and acetic acids and carbohydrates were metabolized most frequently, whereas aerobic respiration I with the use of cytochrome C was the main pathway used by the microbiome of the studied bottom sediments.

Factors affecting seasonal variation of microbial community structure in Hulun Lake, China

Microbial communities play an important role in water quality regulation and biogeochemical cycling in freshwater ecosystems. However, there is a lack of research on the seasonal variation in lake water microorganisms in cold environments. In this study, 16S rRNA gene high-throughput sequencing was used to explore the microbial community and its influencing factors in Hulun Lake water during different seasons. The results showed that Proteobacteria, Actinobacteria, and Bacteroidetes were the most important phyla in the microbial community of Hulun Lake, but they had significant seasonal differences in their distribution. In addition, significant seasonal differences were observed in the α diversity of microorganisms, with bacterial diversity being higher in winter than in summer. Changes in environmental variables were significantly correlated with changes in the microbial community, and the rapid changes in temperature, pH, and dissolved oxygen are potentially the major factors influencing seasonal bacterial diversity trends. The findings of the present study enhance our understanding of the microbial communities in alpine lake ecosystems and are of great significance for the management and protection of lake ecosystems.

Seasonal variations and co-occurrence networks of bacterial communities in the water and sediment of artificial habitat in Laoshan Bay, China

Marine bacteria in the seawater and seafloor are essential parts of Earth’s biodiversity, as they are critical participants of the global energy flow and the material cycles. However, their spatial-temporal variations and potential interactions among varied biotopes in artificial habitat are poorly understood. In this study, we profiled the variations of bacterial communities among seasons and areas in the water and sediment of artificial reefs using 16S rRNA gene sequencing, and analyzed the potential interaction patterns among microorganisms. Distinct bacterial community structures in the two biotopes were exhibited. The Shannon diversity and the richness of phyla in the sediment were higher, while the differences among the four seasons were more evident in the water samples. The seasonal variations of bacterial communities in the water were more distinct, while significant variations among four areas were only observed in the sediment. Correlation analysis revealed that nitrite and mud content were the most important factors influencing the abundant OTUs in the water and sediment, respectively. Potential interactions and keystone species were identified based on the three co-occurrence networks. Results showed that the correlations among bacterial communities in the sediment were lower than in the water. Besides, the abundance of the top five abundant species and five keystone species had different changing patterns among four seasons and four areas. These results enriched our understanding of the microbial structures, dynamics, and interactions of microbial communities in artificial habitats, which could provide new insights into planning, constructing and managing these special habitats in the future.

Impact of anthropogenic organic matter on bacterial community distribution in the continental shelf sediments of southeastern Arabian Sea

The objective of this study was to understand the influence of anthropogenic organic matter on the spatial distribution microbial community in the continental shelf sediments of the Southeastern Arabian Sea (SEAS). The sediment samples were taken from the inner shelf (30 m depths) and outer shelf (100-200 m). The C:N_molar ratio of the sediment displayed a significant variation between the inner and outer shelf and a higher terrestrial organic input in the inner shelf. Microbial community composition also showed a significant variation between the inner and outer shelf (p ≤ 0.05). Proteobacteria was the dominant phylum in the outer shelf sediments (42.5%), whereas Desulfobacterota (21.9%) was the dominant phylum in the inner shelf. Complex terrestrial organic matter degrading bacteria dominated the inner shelf, whereas oligophilic microbial community and autochthonous organic matter utilizing bacteria dominated the outer shelf. Thus the source of organic matter controlled the microbial distribution in the SEAS.