Influence of Land Use,Nutrients, and Geography on Microbial Communities and Fecal Indicator Abundance at Lake Michigan Beaches

Microbial communities within beach sand play a key role in nutrient cycling and are important to the nearshore ecosystem function. Escherichia coli and enterococci, two common indicators of fecal pollution, have been shown to persist in the beach sand, but little is known about how microbial community assemblages are related to these fecal indicator bacteria (FIB) reservoirs. We examined eight beaches across a geographic gradient and range of land use types and characterized the indigenous community structure in the water and the backshore, berm, and submerged sands. FIB were found at similar levels in sand at beaches adjacent to urban, forested, and agricultural land and in both the berm and backshore. However, there were striking differences in the berm and backshore microbial communities, even within the same beach, reflecting the very different environmental conditions in these beach zones in which FIB can survive. In contrast, the microbial communities in a particular beach zone were similar among beaches, including at beaches on opposite shores of Lake Michigan. The differences in the microbial communities that did exist within a beach zone correlated to nutrient levels, which varied among geographic locations. Total organic carbon and total phosphorus were higher in Wisconsin beach sand than in beach sand from Michigan. Within predominate genera, fine-scale sequence differences could be found that distinguished the populations from the two states, suggesting a biogeographic effect. This work demonstrates that microbial communities are reflective of environmental conditions at freshwater beaches and are able to provide useful information regarding long-term anthropogenic stress.     

Indicator microbes correlate with pathogenic bacteria, yeasts and helminthes in sand at a subtropical recreational beach site

Aims: Research into the relationship between pathogens, faecal indicator microbes and environmental factors in beach sand has been limited, yet vital to the understanding of the microbial relationship between sand and the water column and to the improvement of criteria for better human health protection at beaches. The objectives of this study were to evaluate the presence and distribution of pathogens in various zones of beach sand (subtidal, intertidal and supratidal) and to assess their relationship with environmental parameters and indicator microbes at a non‐point source subtropical marine beach. Methods and Results: In this exploratory study in subtropical Miami (Florida, USA), beach sand samples were collected and analysed over the course of 6 days for several pathogens, microbial source tracking markers and indicator microbes. An inverse correlation between moisture content and most indicator microbes was found. Significant associations were identified between some indicator microbes and pathogens (such as nematode larvae and yeasts in the genus Candida), which are from classes of microbes that are rarely evaluated in the context of recreational beach use. Conclusions: Results indicate that indicator microbes may predict the presence of some of the pathogens, in particular helminthes, yeasts and the bacterial pathogen Staphylococcus aureus including methicillin‐resistant forms. Indicator microbes may thus be useful for monitoring beach sand and water quality at non‐point source beaches. Significance and Impact of the Study: The presence of both indicator microbes and pathogens in beach sand provides one possible explanation for human health effects reported at non‐point sources beaches.     

Relationship between Enterococcal Levels and Sediment Biofilms at Recreational Beaches in South Florida

Enterococci, recommended at the U.S. federal level for monitoring water quality at marine recreational beaches, have been found to reside and grow within beach sands. However, the environmental and ecological factors affecting enterococcal persistence remain poorly understood, making it difficult to determine levels of fecal pollution and assess human health risks. Here we document the presence of enterococci associated with beach sediment biofilms at eight south Florida recreational beaches. Enterococcal levels were highest in supratidal sands, where they displayed a nonlinear, unimodal relationship with extracellular polymeric secretions (EPS), the primary component of biofilms. Enterococcal levels peaked at intermediate levels of EPS, suggesting that biofilms may promote the survival of enterococci but also inhibit enterococci as the biofilm develops within beach sands. Analysis of bacterial community profiles determined by terminal restriction fragment length polymorphisms showed the bacterial communities of supratidal sediments to be significantly different from intertidal and subtidal communities; however, no differences were observed in bacterial community compositions associated with different EPS concentrations. Our results suggest that supratidal sands are a microbiologically unique environment favorable for the incorporation and persistence of enterococci within beach sediment biofilms.     

Biogeochemical controls on microbial diversity in seafloor sulphidic sediments

The ultimate fate of hydrothermal sulphides on the seafloor depends on the nature and rate of abiotic and microbially catalysed reactions where sulphide minerals are exposed to oxic seawater. This study combines organic and inorganic geochemical with microbiological measurements across a suboxic transition zone of highly altered sulphidic sediments from the Trans‐Atlantic Geotransverse hydrothermal field to characterize the reaction products and microbial communities present. There is distinct biogeochemical zonation apparent within the sediment sequence from oxic surface layers through a suboxic transition zone into the sulphide material. The microbial communities in the sediment differ significantly between the biogeochemical horizons sampled, with the identified microbes inferred to be associated with Fe and S redox cycling. In particular, Marinobacter species, organisms associated with circumneutral Fe oxidation, are dominant in a sulphide lens present in the lower core. The dominance of Marinobacter‐related sequences within the relict sulphide lens implies that these organisms play an important role in the alteration of sulphides at the seafloor once active venting has ceased.     

Pyrosequencing Characterization of the Microbiota from Atlantic Intertidal Marine Sponges Reveals High Microbial Diversity and the Lack of Co-Occurrence Patterns

Sponges are ancient metazoans that host diverse and complex microbial communities. Sponge-associated microbial diversity has been studied from wide oceans across the globe, particularly in subtidal regions, but the microbial communities from intertidal sponges have remained mostly unexplored. Here we used pyrosequencing to characterize the microbial communities in 12 different co-occurring intertidal marine sponge species sampled from the Atlantic coast, revealing a total of 686 operational taxonomic units (OTUs) at 97% sequence similarity. Taxonomic assignment of 16S ribosomal RNA tag sequences estimated altogether 26 microbial groups, represented by bacterial (75.5%) and archaeal (22%) domains. Proteobacteria (43.4%) and Crenarchaeota (20.6%) were the most dominant microbial groups detected in all the 12 marine sponge species and ambient seawater. The Crenarchaeota microbes detected in three Atlantic Ocean sponges had a close similarity with Crenarchaeota from geographically separated subtidal Red Sea sponges. Our study showed that most of the microbial communities observed in sponges (73%) were also found in the surrounding ambient seawater suggesting possible environmental acquisition and/or horizontal transfer of microbes. Beyond the microbial diversity and community structure assessments (NMDS, ADONIS, ANOSIM), we explored the interactions between the microbial communities coexisting in sponges using the checkerboard score (C-score). Analyses of the microbial association pattern (co-occurrence) among intertidal sympatric sponges revealed the random association of microbes, favoring the hypothesis that the sponge-inhabiting microbes are recruited from the habitat mostly by chance or influenced by environmental factors to benefit the hosts.     

Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline

Deep-sea hypersaline anoxic basins are polyextreme environments in the ocean’s interior characterized by the high density of brines that prevents mixing with the overlaying seawater, generating sharp chemoclines and redoxclines up to tens of meters thick that host a high concentration of microbial communities. Yet, a fundamental understanding of how such pycnoclines shape microbial life and the associated biogeochemical processes at a fine scale, remains elusive. Here, we applied high-precision sampling of the brine–seawater transition interface in the Suakin Deep, located at 2770 m in the central Red Sea, to reveal previously undocumented fine-scale community structuring and succession of metabolic groups along a salinity gradient only 1 m thick. Metagenomic profiling at a 10-cm-scale resolution highlighted spatial organization of key metabolic pathways and corresponding microbial functional units, emphasizing the prominent role and significance of salinity and oxygen in shaping their ecology. Nitrogen cycling processes are especially affected by the redoxcline with ammonia oxidation processes being taxa and layers specific, highlighting also the presence of novel microorganisms, such as novel Thaumarchaeota and anammox, adapted to the changing conditions of the chemocline. The findings render the transition zone as a critical niche for nitrogen cycling, with complementary metabolic networks, in turn underscoring the biogeochemical complexity of deep-sea brines.Subject terms: Microbial ecology, Metagenomics     

Geochemical factors impacting nitrifying communities in sandy sediments

Sandy sediment beaches covering 70% of non-ice-covered coastlines are important ecosystems for nutrient cycling along the land-ocean continuum. Subterranean estuaries (STEs), where groundwater and seawater meet, are hotspots for biogeochemical cycling within sandy beaches. The STE microbial community facilitates biogeochemical reactions, determining the fate of nutrients, including nitrogen (N), supplied by groundwater. Nitrification influences the fate of N, oxidising reduced dissolved inorganic nitrogen (DIN), making it available for N removal. We used metabarcoding of 16S rRNA genes and quantitative PCR (qPCR) of ammonia monooxygenase (amoA) genes to characterise spatial and temporal variation in STE microbial community structure and nitrifying organisms. We examined nitrifier diversity, distribution and abundance to determine how geochemical measurements influenced their distribution in STEs. Sediment microbial communities varied with depth (p-value = 0.001) and followed geochemical gradients in dissolved oxygen (DO), salinity, pH, dissolved inorganic carbon and DIN. Genetic potential for nitrification in the STE was evidenced by qPCR quantification of amoA genes. Ammonia oxidiser abundance was best explained by DIN, DO and pH. Our results suggest that geochemical gradients are tightly linked to STE community composition and nitrifier abundance, which are important to determine the fate and transport of groundwater-derived nutrients to coastal waters.     

Microbes in beach sands: integrating environment,ecology and public health

Beach sand is a habitat that supports many microbes, including viruses, bacteria, fungi and protozoa (micropsammon). The apparently inhospitable conditions of beach sand environments belie the thriving communities found there. Physical factors, such as water availability and protection from insolation; biological factors, such as competition, predation, and biofilm formation; and nutrient availability all contribute to the characteristics of the micropsammon. Sand microbial communities include autochthonous species/phylotypes indigenous to the environment. Allochthonous microbes, including fecal indicator bacteria (FIB) and waterborne pathogens, are deposited via waves, runoff, air, or animals. The fate of these microbes ranges from death, to transient persistence and/or replication, to establishment of thriving populations (naturalization) and integration in the autochthonous community. Transport of the micropsammon within the habitat occurs both horizontally across the beach, and vertically from the sand surface and ground water table, as well as at various scales including interstitial flow within sand pores, sediment transport for particle-associated microbes, and the large-scale processes of wave action and terrestrial runoff. The concept of beach sand as a microbial habitat and reservoir of FIB and pathogens has begun to influence our thinking about human health effects associated with sand exposure and recreational water use. A variety of pathogens have been reported from beach sands, and recent epidemiology studies have found some evidence of health risks associated with sand exposure. Persistent or replicating populations of FIB and enteric pathogens have consequences for watershed/beach management strategies and regulatory standards for safe beaches. This review summarizes our understanding of the community structure, ecology, fate, transport, and public health implications of microbes in beach sand. It concludes with recommendations for future work in this vastly under-studied area.     

南极冰下水生态系统微生物与生源元素循环研究进展

南极大陆冰盖下存在液态水,形成了由冰下湖、冰下河/溪、冰封湖和冰架下水体等组成的冰下水生态系统,具有低温、黑暗和寡营养等极端的环境条件特征。微生物主导了南极冰下水生态系统,其具有丰富多样的种群构成、功能形式和独特的适应机制,在生源元素生物地球化学循环过程中起了重要作用。研究南极冰下微生物群落的生态特征及其参与的生源元素地球化学循环过程,可为揭示地球生命演化和探索外星生命提供指示,具有重要的科学意义。本文综述了南极冰下水生态系统的极端环境条件、冰下微生物的多样性、冰下微生物参与的生物地球化学循环以及冰下微生物的适极机理,最后基于研究现状展望了南极冰下微生物的未来研究方向。     

Responses of Bacterial Communities to Simulated Climate Changes in Alpine Meadow Soil of the Qinghai-Tibet Plateau

The soil microbial community plays an important role in terrestrial carbon and nitrogen cycling. However, microbial responses to climate warming or cooling remain poorly understood, limiting our ability to predict the consequences of future climate changes. To address this issue, it is critical to identify microbes sensitive to climate change and key driving factors shifting microbial communities. In this study, alpine soil transplant experiments were conducted downward or upward along an elevation gradient between 3,200 and 3,800 m in the Qinghai-Tibet plateau to simulate climate warming or cooling. After a 2-year soil transplant experiment, soil bacterial communities were analyzed by pyrosequencing of 16S rRNA gene amplicons. The results showed that the transplanted soil bacterial communities became more similar to those in their destination sites and more different from those in their “home” sites. Warming led to increases in the relative abundances in Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria and decreases in Acidobacteria, Betaproteobacteria, and Deltaproteobacteria, while cooling had opposite effects on bacterial communities (symmetric response). Soil temperature and plant biomass contributed significantly to shaping the bacterial community structure. Overall, climate warming or cooling shifted the soil bacterial community structure mainly through species sorting, and such a shift might correlate to important biogeochemical processes such as greenhouse gas emissions. This study provides new insights into our understanding of soil bacterial community responses to climate warming and cooling.     

海岸带地区的固氮、氨化、硝化与反硝化特征

海岸带是海洋环境中受人类活动影响最大、生物地球化学循环最为活跃的地区。这一地区氮的生物地球化学循环包括 :生物固氮、有机氮的氨化、氮的硝化、反硝化等 4个主要过程。概括性地介绍了有关这四个过程的发生机制、环境影响因素及研究方法等方面的研究动态、进展、存在的科学问题与今后的研究方向。过去十几年来 ,固氮主要集中在对束毛藻属的研究上 ,其间有两个重要发现 ,一是生物固氮在海洋氮循环中的作用远比人们以前的想象要重要得多 ;二是蓝细菌已经在海洋中存在了 2 0亿年 ,它们有可能调节大气中的 CO2 ,进而影响全球气候。由于有机物的结构千差万别 ,含氮有机物的氨化过程可能是一个简单的矿化反应 ,也有可能是一系列复杂的代谢过程 ,在水解酶的作用下含氮有机物降解为下一级化合物。硝化过程分两步进行 ,氨的硝化为反硝化细菌提供了重要的硝酸盐来源 ,通常采用同位素方法来研究硝化过程。发生在沉积物中的反硝化过程是氮循环的关键步骤 ,反硝化过程一方面减少了海水中初级生产者可利用的氮 ,另一方面产生了终结产物 N2 和 N2 O,而 N2 O是一种温室气体 ,可能影响全球气候变化     

A metabarcoding analysis of the wrackbed microbiome indicates a phylogeographic break along the North Sea–Baltic Sea transition zone

Sandy beaches are biogeochemical hotspots that bridge marine and terrestrial ecosystems via the transfer of organic matter, such as seaweed (termed wrack). A keystone of this unique ecosystem is the microbial community, which helps to degrade wrack and re-mineralize nutrients. However, little is known about this community. Here, we characterize the wrackbed microbiome as well as the microbiome of a primary consumer, the seaweed fly Coelopa frigida, and examine how they change along one of the most studied ecological gradients in the world, the transition from the marine North Sea to the brackish Baltic Sea. We found that polysaccharide degraders dominated both microbiomes, but there were still consistent differences between wrackbed and fly samples. Furthermore, we observed a shift in both microbial communities and functionality between the North and Baltic Sea driven by changes in the frequency of different groups of known polysaccharide degraders. We hypothesize that microbes were selected for their abilities to degrade different polysaccharides corresponding to a shift in polysaccharide content in the different seaweed communities. Our results reveal the complexities of both the wrackbed microbial community, with different groups specialized to different roles, and the cascading trophic consequences of shifts in the near shore algal community.     

Fate of Heterotrophic Microbes in Pelagic Habitats: Focus on Populations

Major biogeochemical processes in the water columns of lakes and oceans are related to the activities of heterotrophic microbes, e.g., the mineralization of organic carbon from photosynthesis and allochthonous influx or its transport to the higher trophic levels. During the last 15 years, cultivation-independent molecular techniques have substantially contributed to our understanding of the diversity of the microbial communities in different aquatic systems. In parallel, the complexity of aquatic habitats at a microscale has inspired research on the ecophysiological properties of uncultured microorganisms that thrive in a continuum of dissolved to particulate organic matter. One possibility to link these two aspects is to adopt a “Gleasonian” perspective, i.e., to study aquatic microbial assemblages in situ at the population level rather than looking at microbial community structure, diversity, or function as a whole. This review compiles current knowledge about the role and fate of different populations of heterotrophic picoplankton in marine and inland waters. Specifically, we focus on a growing suite of techniques that link the analysis of bacterial identity with growth, morphology, and various physiological activities at the level of single cells. An overview is given of the potential and limitations of methodological approaches, and factors that might control the population sizes of different microbes in pelagic habitats are discussed.     

Coupling between macroalgal inputs and nutrients outcrop in exposed sandy beaches

Fluxes of nutrients across habitats are of paramount relevance in ecological studies due to the implication in primary production, trophic structure and biodiversity. This study analyses the role of sandy beaches in the processing of organic matter. Three beaches with different macroalgal inputs were sampled throughout the annual cycle. The standing stock of wrack macroalgae on the beach surface and the nutrient concentration in the intertidal pore water (IPW) and in the surf zone water were measured monthly. Mean concentration of dissolved inorganic nitrogen and phosphate in the IPW increased from the low to the very high subsidized beach. Seasonal coupling was observed between the wrack biomass and the nutrient concentration throughout the year. Among the nutrient species, a variable relationship was found between the NH₄ ⁺/NO _x ^? ratio and the biomass of macroalgae deposited. These results provide evidences of the active role of sandy beaches in the processing of organic matter and in the nutrient cycling, remarking the feedback connectivity between sandy beaches and their neighbour ecosystems.     

Neutrophilic Iron-Oxidizing Bacteria in the Ocean: Their Habitats,Diversity, and Roles in Mineral Deposition,Rock Alteration,and Biomass Production in the Deep-Sea

The importance of metals to life has long been appreciated. Iron (Fe) is the fourth most abundant element overall, and the second most abundant element that is redox-active in near-surface aqueous habitats, rendering it the most important environmental metal. While it has long been recognized that microorganisms participate in the global iron cycle, appreciation for the pivotal role that redox cycling of iron plays in energy conservation among diverse prokaryotes has grown substantially in the past decade. In addition, redox reactions involving Fe are linked to several other biogeochemical cycles (e.g., carbon), with significant ecological ramifications. The increasing appreciation for the role of microbes in redox transformations of Fe is reflected in a recent surge in biological and environmental studies of microorganisms that conserve energy for growth from redox cycling of Fe compounds, particularly in the deep ocean. Here we highlight some of the key habitats where microbial Fe-oxidation plays significant ecological and biogeochemical roles in the oceanic regime, and provide a synthesis of recent studies concerning this important physiological group. We also provide the first evidence that microbial Fe-oxidizing bacteria are a critical factor in the kinetics of mineral dissolution at the seafloor, by accelerating dissolution by 6–8 times over abiotic rates. We assert that these recent studies, which indicate that microbial Fe-oxidation is widespread in the deep-sea, combined with the apparent role that this group play in promoting rock and mineral weathering, indicate that a great deal more attention to these microorganisms is warranted in order to elucidate the full physiological and phylogenetic diversity and activity of the neutrophilic Fe-oxidizing bacteria in the oceans.     

Carbon and nitrogen biogeochemical cycling potentials of supraglacial cryoconite communities

Microorganisms have a crucial role to play in the cycling of nutrients within glacial environments. These systems are often nutrient-limited, and so biogeochemical reactions, which ensure the availability of nutrients for microbial communities, are critical for the maintenance of these systems. This study uses molecular biology to characterise the supraglacial cryoconite microbial communities that are capable of cycling carbon and nitrogen in a range of glacial environments. Organisms with the potential to photosynthesise were identified, including Cyanobacteria, Actinobacteria, Betaproteobacteria, Stramenopiles and Haptophyceae. Organisms with the potential to perform nitrification and denitrification processes were also identified and featured Betaproteobacteria, Alphaproteobacteria, Thaumarchaeota and Cyanobacteria. While it is unlikely that the chemical and physical parameters of the supraglacial environment will facilitate optimal rates of all of the nitrogen-related biogeochemical processes, the transport of these cryoconite communities to downstream locations, where more favourable conditions may prevail, will perhaps provide a valuable inoculation of microorganisms with the genetic potential to catalyse these reactions elsewhere.     

微生物在珊瑚礁生态系统中的作用与功能

珊瑚礁是由珊瑚、鱼类、底栖生物、藻类以及微生物等多种生命形式组成的聚集体,代表着一类典型的海洋生态系统.珊瑚礁存在于热带和亚热带的寡营养环境,拥有极高的初级生产力和生产效率,被誉为“海底热带雨林”.微生物在珊瑚礁生态系统的生物地球化学循环、物质转化以及健康维护上具有重要作用.随着分子生态学的发展,微生物在珊瑚中的作用和功能日益凸显.本文总结了微生物生态学的研究现状,包括珊瑚生态系统中微生物的定植方式,共生微生物的特性(专一性、可塑性、协同进化),共生微生物与珊瑚疾病的关系与信号调节,以及微生物应对全球变化(气温升高、海水酸化、富营养化)的响应.从“珊瑚 微生物”共生体的发生、共生微生物的特性与生态功能,以及全球环境变化下微生物的衍生效应来梳理最新理论与成果,明确珊瑚微生物生态学机制,为更好地保护珊瑚资源、维护海洋生物多样性提供理论借鉴.     

Electron acceptors for anaerobic oxidation of methane drive microbial community structure and diversity in mud volcanoes

Mud volcanoes (MVs) emit globally significant quantities of methane into the atmosphere, however, methane cycling in such environments is not yet fully understood, as the roles of microbes and their associated biogeochemical processes have been largely overlooked. Here, we used data from high‐throughput sequencing of microbial 16S rRNA gene amplicons from six MVs in the Junggar Basin in northwest China to quantify patterns of diversity and characterize the community structure of archaea and bacteria. We found anaerobic methanotrophs and diverse sulfate‐ and iron‐reducing microbes in all of the samples, and the diversity of both archaeal and bacterial communities was strongly linked to the concentrations of sulfate, iron and nitrate, which could act as electron acceptors in anaerobic oxidation of methane (AOM). The impacts of sulfate/iron/nitrate on AOM in the MVs were verified by microcosm experiments. Further, two representative MVs were selected to explore the microbial interactions based on phylogenetic molecular ecological networks. The sites showed distinct network structures, key species and microbial interactions, with more complex and numerous linkages between methane‐cycling microbes and their partners being observed in the iron/sulfate‐rich MV. These findings suggest that electron acceptors are important factors driving the structure of microbial communities in these methane‐rich environments.     

气候变暖下水圈甲烷排放及其微生物学机制

大气温室气体浓度升高导致的气候变暖已对人类社会可持续发展带来了严重影响。水圈生态系统既是全球最为重要的碳汇之一,也是全球最为重要的甲烷自然排放源。因此,阐明气候变暖背景下水圈甲烷排放格局及其相关微生物调控机制,是认识未来地球气候系统演变机理、预测未来全球变化潜在情景的关键命题,也将为如何高效发挥水圈碳汇潜力提供基础理论支撑,更好应对全球气候变化问题。本文主要综述了气候变暖背景下主要水圈生态系统中微生物介导的甲烷排放研究的现状与趋势,介绍了水圈甲烷排放格局及其气候变暖背景下的演变趋势,回顾了气候变暖对甲烷代谢相关微生物群落与功能的复杂调控作用。基于目前的研究现状,未来亟需通过微观机制与宏观过程相结合的途径,并基于生态系统复杂性和气候变暖长期性开展相关研究。同时,建议应加强对海洋等相对薄弱区域的研究。     

湖泊硫循环微生物研究进展

湖泊是响应气候和环境变化的关键生态系统,是研究元素(如碳、氮和硫等)生物地球化学循环的热点环境。湖泊(尤其咸盐湖)具有硫酸盐含量高且含硫化合物种类丰富的特点,因而湖泊中硫元素生物地球化学循环过程非常活跃。微生物是驱动湖泊硫循环的重要推手。因此,研究湖泊中微生物参与的硫元素生物地球化学循环过程以及相关微生物类群构成,对于深入探索微生物在湖泊生态系统中的作用具有重要意义。本文综述了湖泊中驱动硫循环的微生物(硫氧化菌和硫酸盐还原菌)种群多样性、功能基因、代谢途径、硫氧化/硫酸盐还原速率及其对环境条件变化响应等方面的研究现状,并对未来湖泊微生物驱动的硫循环研究方向进行了展望。