尿素肥斑扩散对土壤微生物群落结构的影响

磷脂脂肪酸 (PL FA)被认为是有效指示活体土壤微生物群落结构变化的标记物之一 ,该方法已在土壤微生物的研究中被大量应用。采用特制容器 ,模拟尿素肥斑在土壤中的扩散行为 ,观察距尿素肥斑不同距离微域中养分形态和浓度变化及其对土壤微生物群落结构的影响。试验结果表明 ,培养 7d后 ,No.7(距肥斑 7cm)和 No.8(距肥斑 8cm )微域的 NH 4、NO- 2 、NO- 3浓度最高 ,NO- 2 是尿素扩散区域的主要离子存在形态。对提取到的 2 5种 PL FA进行主成分分析 (PCA) ,发现 PL FA组成随不同微域养分浓度变化而变化 ,说明微生物群落结构发生了改变。就标记性 PL FA而言 ,尿素扩散导致真菌 PL FA在高浓度养分微域浓度增加 ,细菌 PL FA浓度下降 ,其中 ,No.7微域的真菌 PL FA18∶ 2ω6 ,9和 PL FA18∶ 1ω9浓度分别比对照 (No.2 0微域 )增加 173%和 4 7.2 %。然而 ,放线菌 PL FA 10 Me18∶ 0浓度变化不大     

Spatial variability of marine bacterial and archaeal communities along the particulate matter continuum

Biotic and abiotic particles shape the microspatial architecture that defines the microbial aquatic habitat, being particles highly variable in size and quality along oceanic horizontal and vertical gradients. We analysed the prokaryotic (bacterial and archaeal) diversity and community composition present in six distinct particle size classes ranging from the pico‐ to the microscale (0.2 to 200 μm). Further, we studied their variations along oceanographic horizontal (from the coast to open oceanic waters) and vertical (from the ocean surface into the meso‐ and bathypelagic ocean) gradients. In general, prokaryotic community composition was more variable with depth than in the transition from the coast to the open ocean. Comparing the six size‐fractions, distinct prokaryotic communities were detected in each size‐fraction, and whereas bacteria were more diverse in the larger size‐fractions, archaea were more diverse in the smaller size‐fractions. Comparison of prokaryotic community composition among particle size‐fractions showed that most, but not all, taxonomic groups have a preference for a certain size‐fraction sustained with depth. Species sorting, or the presence of diverse ecotypes with distinct size‐fraction preferences, may explain why this trend is not conserved in all taxa.     

Spatial distribution of viruses associated with planktonic and attached microbial communities in hydrothermal environments

Viruses play important roles in marine surface ecosystems, but little is known about viral ecology and virus-mediated processes in deep-sea hydrothermal microbial communities. In this study, we examined virus-like particle (VLP) abundances in planktonic and attached microbial communities, which occur in physical and chemical gradients in both deep and shallow submarine hydrothermal environments (mixing waters between hydrothermal fluids and ambient seawater and dense microbial communities attached to chimney surface areas or macrofaunal bodies and colonies). We found that viruses were widely distributed in a variety of hydrothermal microbial habitats, with the exception of the interior parts of hydrothermal chimney structures. The VLP abundance and VLP-to-prokaryote ratio (VPR) in the planktonic habitats increased as the ratio of hydrothermal fluid to mixing water increased. On the other hand, the VLP abundance in attached microbial communities was significantly and positively correlated with the whole prokaryotic abundance; however, the VPRs were always much lower than those for the surrounding hydrothermal waters. This is the first report to show VLP abundance in the attached microbial communities of submarine hydrothermal environments, which presented VPR values significantly lower than those in planktonic microbial communities reported before. These results suggested that viral lifestyles (e.g., lysogenic prevalence) and virus interactions with prokaryotes are significantly different among the planktonic and attached microbial communities that are developing in the submarine hydrothermal environments.     

Geochemistry of Virus–Prokaryote Interactions in Freshwater and Acid Mine Drainage Environments,Ontario, Canada

An extensive water sample survey was conducted in southern Ontario, Canada across a variety of freshwater systems in order to further understand the role of viruses in aquatic environments. Backwards stepwise multiple regression analysis found that VLP (virus-like particle) abundance, phosphate, pH, sulfate, and magnesium are predictors of prokaryotic abundance with the model describing 90% of the variability in the data (R² = 0.90). Statistically significant (P < 0.05) predictors of VLP abundance were mineral saturation indices (SI) of goethite (R² = 0.78) although moderate Pearson component analysis correlations (r) were noted with ferrihydrite, jarosite, and pyrolusite. These relationships indicate that viral inactivation through mineral attachment may be a contributor to the moderate relationship between VLP and prokaryotic abundance (r_s = 0.45). In addition, VLP abundance is shown to have a stronger correlation with minerals SI values than prokaryotes indicating a stronger mineral influence with viruses.     

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.     

Microbiology of flooded rice paddies

Flooded rice paddies are one of the major biogenic sources of atmospheric methane. Apart from this contribution to the 'greenhouse' effect, rice paddy soil represents a suitable model system to study fundamental aspects of microbial ecology, such as diversity, structure, and dynamics of microbial communities as well as structure-function relationships between microbial groups. Flooded rice paddy soil can be considered as a system with three compartments (oxic surface soil, anoxic bulk soil, and rhizosphere) characterized by different physio-chemical conditions. After flooding, oxygen is rapidly depleted in the bulk soil. Anaerobic microorganisms, such as fermentative bacteria and methanogenic archaea, predominate within the microbial community, and thus methane is the final product of anaerobic degradation of organic matter. In the surface soil and the rhizosphere well-defined microscale chemical gradients can be measured. The oxygen profile seems to govern gradients of other electron acceptors (e.g., nitrate, iron(III), and sulfate) and reduced compounds (e.g., ammonium, iron(II), and sulfide). These gradients provide information about the activity and spatial distribution of functional groups of microorganisms. This review presents the current knowledge about the highly complex microbiology of flooded rice paddies. In Section 2 we describe the predominant microbial groups and their function with particular regard to bacterial populations utilizing polysaccharides and simple sugars, and to the methanogenic archaea. Section 3 describes the spatial and temporal development of microscale chemical gradients measured in experimentally defined model systems, including gradients of oxygen and dissolved and solid-phase iron(III) and iron(II). In Section 4, the results of measurements of microscale gradients of oxygen, pH, nitrate-nitrite, and methane in natural rice fields and natural rice soil cores taken to the laboratory will be presented. Finally, perspectives of future research are discussed (Section 5).     

Uniform selective pressures within redox zones drive gradual changes in microbial community composition in hadal sediments

Microbial communities in marine sediments are highly diverse, yet the processes that give rise to this complexity are unclear. It has been proposed that benthic microbial communities must be continuously re-seeded from the water column because dispersal within the sediment is severely limited. Previous studies consistently report that the composition of the microbial community gradually changes with sediment depth. However, the relative contributions of the processes that underlie these compositional gradients have not been determined, and it is unknown whether microbial dispersal is indeed too slow to outpace burial. Here, we applied ecological statistical frameworks to 16S rRNA gene amplicon-based community composition data from Atacama Trench sediments to investigate the links between biogeochemistry, burial, and microbial community assembly processes. We confirm that dispersal limitation affects microbial communities and find that gradual changes in community composition are driven by selective pressures that change abruptly across the discrete boundaries between redox zones rather than along continuous biogeochemical gradients, while selective pressures are uniform within each zone. The gradual changes in community composition over centimetres of depth within a zone hence reflects a decades-long response to the abruptly changing selective pressures.     

Temporal and Spatial Distribution of the Microbial Community of Winogradsky Columns

Winogradsky columns are model microbial ecosystems prepared by adding pond sediment to a clear cylinder with additional supplements and incubated with light. Environmental gradients develop within the column creating diverse niches that allow enrichment of specific bacteria. The enrichment culture can be used to study soil and sediment microbial community structure and function. In this study we used a 16S rRNA gene survey to characterize the microbial community dynamics during Winogradsky column development to determine the rate and extent of change from the source sediment community. Over a period of 60 days, the microbial community changed from the founding pond sediment population: Cyanobacteria, Chloroflexi, Nitrospirae, and Planctomycetes increased in relative abundance over time, while most Proteobacteria decreased in relative abundance. A unique, light-dependent surface biofilm community formed by 60 days that was less diverse and dominated by a few highly abundant bacteria. 67–72% of the surface community was comprised of highly enriched taxa that were rare in the source pond sediment, including the Cyanobacteria Anabaena, a member of the Gemmatimonadetes phylum, and a member of the Chloroflexi class Anaerolinea. This indicates that rare taxa can become abundant under appropriate environmental conditions and supports the hypothesis that rare taxa serve as a microbial seed bank. We also present preliminary findings that suggest that bacteriophages may be active in the Winogradsky community. The dynamics of certain taxa, most notably the Cyanobacteria, showed a bloom-and-decline pattern, consistent with bacteriophage predation as predicted in the kill-the-winner hypothesis. Time-lapse photography also supported the possibility of bacteriophage activity, revealing a pattern of colony clearance similar to formation of viral plaques. The Winogradsky column, a technique developed early in the history of microbial ecology to enrich soil microbes, may therefore be a useful model system to investigate both microbial and viral ecology.     

Structure and seasonal dynamics of hyporheic zone microbial communities in free-stone rivers of the estern United States

The hyporheic zone of a river is characterized by being nonphotic, exhibiting chemical/redox gradients, and having a heterotrophic food web based on the consumption of organic carbon entrained from surface waters. Hyporheic microbial communities constitute the base of food webs in these environments and are important for maintaining a functioning lotic ecosystem. While microbial communities of rivers dominated by fine-grained sediments are relatively well studied, little is known about the structure and seasonal dynamics of microbial communities inhabiting the predominantly gravel and cobble hyporheic zones of rivers of the western United States. Here, we present the first molecular analysis of hyporheic microbial communities of three different stream types (based on mean base discharge, substratum type, and drainage area), in Montana. Utilizing 16S rDNA phylogeny, DGGE pattern analysis, and qPCR, we have analyzed the prokaryotic communities living on the 1.7 to 2.36 mm grain-size fraction of hyporheic sediments from three separate riffles in each stream. DGGE analysis showed clear seasonal community patterns, indicated similar community composition between different riffles within a stream (95.6–96.6% similarity), and allowed differentiation between communities in different streams. Each river supported a unique complement of species; however, several phylogenetic groups were conserved between all three streams including Pseudomonads and members of the genera Aquabacterium, Rhodoferax, Hyphomicrobium, and Pirellula. Each group showed pronounced seasonal trends in abundance, with peaks during the Fall. The Hyphomicrobium group was numerically dominant throughout the year in all three streams. This work provides a framework for investigating the effects of various environmental factors and anthropogenic effects on microbial communities inhabiting the hyporheic zone.     

Using high-throughput sequencing to assess the impacts of treated and untreated wastewater discharge on prokaryotic communities in an urban river

In many megacities wastewater is an important source of surface water, particularly during drought periods. While changes in surface water chemistry associated with effluent inflow have generally been well-studied, few data have been collected on the effects to prokaryotic communities. The objective of this study was to explore the impacts of treated and untreated wastewater discharges on prokaryotic community in an urban river. High-throughput sequencing was conducted for analyzing the prokaryotic community composition and function in river water, treated wastewater and untreated wastewater. Results revealed that the prokaryotic community compositions in the upstream river reach were dominated by treated wastewater discharge. In the middle- and downstream river reaches, untreated effluent volumes are higher, thus affecting the structure of the prokaryotic community, promoting a rise in Cyanobacteria and Thaumarchaeota. Function annotation revealed a number of genes associated with xenobiotic metabolism and human diseases were observed in river and wastewater samples, suggesting wastewater discharge to river may pose a risk to human health. Quantitative real-time PCR results revealed that the treated and untreated wastewater discharges also affected the abundance of ammonia oxidation bacteria (AOB) and ammonia oxidation archaea (AOA) in river.     

In-depth analyses of marine microbial community genomics

Marine microbes have evolved to live along extreme environmental gradients, whether at the microscale, in proximity to particles or over the entire water column. Using community genomics, DeLong et al. highlight deduced biological differences that result from open-ocean depth gradients. The power of the large-insert libraries used is that both phylogeny and function can be inferred from the genetic material obtained--even for uncultured microbes. Together with complete genomes of marine isolates and advances in physiology and ecology, this study paves the way for ecosystems biology approaches to dynamics and controls of marine microbial populations.     

若尔盖退化泥炭地土壤原核微生物群落结构对水位恢复的短期响应

退化泥炭地的恢复是目前受关注的重要环境问题。若尔盖退化泥炭地原核微生物群落结构对水位恢复的早期响应可以为其生态恢复提供理论依据。为探究原核微生物群落结构对水位恢复的短期响应, 该研究以若尔盖退化泥炭地为研究对象, 设置水位恢复(10和30 cm)和对照组(-10 cm), 进行了1年野外原位水位恢复试验。采集0-15 cm土壤样品, 测定土壤有机碳(SOC)、总氮(TN)、总磷(TP)含量和pH等化学性质, 采用16S rRNA基因高通量测序技术分析微生物群落结构。结果表明: 水位恢复一定程度上能提高SOC、TN、TP含量及其化学计量比, 但与对照组差异不显著。主要优势微生物在门水平为酸杆菌(Acidobacteria)、变形菌(Proteobacteria)和疣微菌(Verrucomicrobia)。短期水位恢复(10和30 cm)对土壤原核微生物的α多样性没有显著影响, 而只是显著降低疣微菌和Spartobacteria的相对丰度, 增加了产甲烷菌种类。疣微菌和Spartobacteria相对丰度与水位和土壤pH呈显著负相关关系。退化泥炭地水位恢复过程中原核微生物群落结构对C:P、N:P和SOC含量响应较为敏感。综上, 短期水位恢复没有改变原核微生物α多样性, 而主要降低了疣微菌和Spartobacteria的相对丰度, 增加了产甲烷菌种类, 这将可能导致甲烷产生途径发生变化。土壤C:P、N:P和SOC含量控制了退化泥炭地随短期水位恢复过程中原核微生物群落结构变异。该研究在一定程度上丰富了原核微生物群落结构对短期水位响应的认识。     

Geospatial insights into the controls of microbialite formation at Laguna Negra,Argentina

Microbialites provide a record of the interaction of microorganisms with their environment constituting a record of microbial life and environments through geologic time. Our capacity to interpret this record is limited by an incomplete understanding of the microbial, geochemical, and physical processes that influence microbialite formation and morphogenesis. The modern system Laguna Negra in Catamarca Province, Argentina contains microbialites in a zone of carbonate precipitation associated with physico-chemical gradients and variable microbial community structure, making it an ideal location to study how these processes interact to drive microbialite formation. In this study, we investigated the geospatial relationships between carbonate morphology, geochemistry, and microbial community at the macro- (decimeter) to mega- (meter) scale by combining high-resolution imagery with field observations. We mapped the distribution of carbonate morphologies and allochtonously-derived volcaniclasts and correlated these with sedimentary matrices and geochemical parameters. Our work shows that the macroscale distribution of different carbonate morphologies spatially correlates with microbial mat distributions—a result consistent with previous microscale observations. Specifically, microbialitic carbonate morphologies more commonly occur associated with microbial mats while abiotically derived carbonate morphologies were less commonly associated with microbial mats. Spatial variability in the size and abundance of mineralized structures was also observed, however, the processes controlling this variability remains unclear and likely represent a combination of microbial, geochemical, and physical processes. Likewise, the processes controlling the spatial distribution of microbial mats at Laguna Negra are also unresolved. Our results suggest that in addition to the physical drivers observed in other modern environments, variability in the spatial distribution of microbialites and other carbonate morphologies at the macro- to megascale can be controlled by microbial processes. Overall, this study provides insight into the interpretation of microbialite occurrence and distributions in the geologic record and highlights the utility of geospatial statistics to probe the controls of microbialite formation in other environments.     

Differences in Hyporheic-Zone Microbial Community Structure along a Heavy-Metal Contamination Gradient

The hyporheic zone of a river is nonphotic, has steep chemical and redox gradients, and has a heterotrophic food web based on the consumption of organic carbon entrained from downwelling surface water or from upwelling groundwater. The microbial communities in the hyporheic zone are an important component of these heterotrophic food webs and perform essential functions in lotic ecosystems. Using a suite of methods (denaturing gradient gel electrophoresis, 16S rRNA phylogeny, phospholipid fatty acid analysis, direct microscopic enumeration, and quantitative PCR), we compared the microbial communities inhabiting the hyporheic zone of six different river sites that encompass a wide range of sediment metal loads resulting from large base-metal mining activity in the region. There was no correlation between sediment metal content and the total hyporheic microbial biomass present within each site. However, microbial community structure showed a significant linear relationship with the sediment metal loads. The abundances of four phylogenetic groups (groups I, II, III, and IV) most closely related to α-, β-, and γ-proteobacteria and the cyanobacteria, respectively, were determined. The sediment metal content gradient was positively correlated with group III abundance and negatively correlated with group II abundance. No correlation was apparent with regard to group I or IV abundance. This is the first documentation of a relationship between fluvially deposited heavy-metal contamination and hyporheic microbial community structure. The information presented here may be useful in predicting long-term effects of heavy-metal contamination in streams and provides a basis for further studies of metal effects on hyporheic microbial communities.     

Feeding preference as a main determinant of microscale patchiness among terrestrial nematodes

Soil biota are responsible for essential ecosystem services such as carbon storage, nutrient cycling and water retention. However, assessment of the condition of soil biota is hampered by an overwhelming level of diversity. With representatives in all trophic levels of the food web, nematode communities can be used as bioindicators. Accurate assessment of nematode assemblages requires insight into the distribution of specimens with distinct food preferences. With the availability of taxon‐specific quantitative PCR assays, distribution patterns of multiple nematode groups can be investigated simultaneously. Here, microscale patchiness of 45 nematode taxa was studied on 12 sampling sites (each with four adjacent microplots) located on arable fields or semi‐natural grasslands (‘system’), and on marine, river clay or sandy soils (‘soil type’). From each microplot, five composite samples were collected. Contrary to our expectations, an increase in the number of cores per composite sample did not result in more accurate measurements, and apparently the levels of microscale patchiness of the taxa are low compared to what has been reported for oligophagous plant‐parasites. System and soil type did not affect microscale distribution. To investigate the level of patchiness in more detail, detection probability (DP) and variability of abundances were calculated. Common and widespread bacterivorous and fungivorous taxa had DP ≥ 90%, confirming low level of microscale patchiness. With DPs of 40%–70%, predators and most omnivores showed degrees of local clustering. An overview of mean variabilities of abundances is presented that offers insight into how feeding preferences impact the microscale distribution both between and within trophic groups.     

Characterizing microbial communities and processes in a modern stromatolite (Shark Bay) using lipid biomarkers and two‐dimensional distributions of porewater solutes

Modern microbial mats are highly complex and dynamic ecosystems. Diffusive equilibration in thin films (DET) and diffusive gradients in thin films (DGT) samplers were deployed in a modern smooth microbial mat from Shark Bay in order to observe, for the first time, two‐dimensional distributions of porewater solutes during day and night time. Two‐dimensional sulfide and alkalinity distributions revealed a strong spatial heterogeneity and a minor contribution of sulfide to alkalinity. Phosphate distributions were also very heterogeneous, while iron(II) distributions were quite similar during day and night with a few hotspots of mobilization. Lipid biomarkers from the three successive layers of the mat were also analysed in order to characterize the microbial communities regulating analyte distributions. The major hydrocarbon products detected in all layers included n‐alkanes and isoprenoids, whilst other important biomarkers included hopanoids. Phospholipid fatty acid profiles revealed a decrease in cyanobacterial markers with depth, whereas sulfate‐reducing bacteria markers increased in abundance in accordance with rising sulfide concentrations with depth. Despite the general depth trends in community structure and physiochemical conditions within the mat, two‐dimensional solute distributions showed considerable small‐scale lateral variability, indicating that the distributions and activities of the microbial communities regulating these solute distributions were equally heterogeneous and complex.     

Differences in hyporheic-zone microbial community structure along a heavy-metal contamination gradient

The hyporheic zone of a river is nonphotic, has steep chemical and redox gradients, and has a heterotrophic food web based on the consumption of organic carbon entrained from downwelling surface water or from upwelling groundwater. The microbial communities in the hyporheic zone are an important component of these heterotrophic food webs and perform essential functions in lotic ecosystems. Using a suite of methods (denaturing gradient gel electrophoresis, 16S rRNA phylogeny, phospholipid fatty acid analysis, direct microscopic enumeration, and quantitative PCR), we compared the microbial communities inhabiting the hyporheic zone of six different river sites that encompass a wide range of sediment metal loads resulting from large base-metal mining activity in the region. There was no correlation between sediment metal content and the total hyporheic microbial biomass present within each site. However, microbial community structure showed a significant linear relationship with the sediment metal loads. The abundances of four phylogenetic groups (groups I, II, III, and IV) most closely related to alpha-, beta-, and gamma-proteobacteria and the cyanobacteria, respectively, were determined. The sediment metal content gradient was positively correlated with group III abundance and negatively correlated with group II abundance. No correlation was apparent with regard to group I or IV abundance. This is the first documentation of a relationship between fluvially deposited heavy-metal contamination and hyporheic microbial community structure. The information presented here may be useful in predicting long-term effects of heavy-metal contamination in streams and provides a basis for further studies of metal effects on hyporheic microbial communities.     

Does bird community structure vary with landscape patchiness? A Chihuahuan Desert perspective

During the springs of 1995–1997, we studied birds and landscapes at 70 sites in the Chihuahuan Desert to assess relations between bird community structure and landscape patchiness. Within each of two spatial extents (1‐km and 2‐km‐radius areas centered on each site), we measured the number of patches of individual land‐cover types and the total number of patches of all land‐cover types. Mean bird richness, and the mean abundance and probability of occurrence of most bird species were significantly correlated with one or more of these variables. Contrary to evidence from other systems, positive association with landscape patchiness did not increase with the degree to which species were habitat generalists, was not negatively related to body size, and did not differ between neotropical migrants and nonmigrants. For the communities’ primary constituent species as a group, the strength of positive and negative associations with patchiness did not differ between landscape extents. Within the 1‐km but not the 2‐km extent, habitat specialists were more positively and negatively associated with patchiness than were habitat generalists. In general, however, neither habitat breadth, body size, nor migratory status seemed to be responsible for associations with landscape patchiness. Mean richness, and the mean abundance and probability of occurrence of most species were significantly correlated with patchiness within one or both extents, and patchiness of all of the most extensive land‐cover types was influential. The simplest explanation for most of the bird‐patchiness relations we found is that the associations reflected species‐specific habitat needs. Through effects on avian richness, abundance, and occurrence, landscape patchiness affected bird community structure. A more complete understanding of the effects of landscape patchiness on bird community structure is likely to emerge when ecologists study the patchiness of major land‐cover types at various spatial extents.     

Contrasting taxonomic stratification of microbial communities in two hypersaline meromictic lakes

Hypersaline meromictic lakes are extreme environments in which water stratification is associated with powerful physicochemical gradients and high salt concentrations. Furthermore, their physical stability coupled with vertical water column partitioning makes them important research model systems in microbial niche differentiation and biogeochemical cycling. Here, we compare the prokaryotic assemblages from Ursu and Fara Fund hypersaline meromictic lakes (Transylvanian Basin, Romania) in relation to their limnological factors and infer their role in elemental cycling by matching taxa to known taxon-specific biogeochemical functions. To assess the composition and structure of prokaryotic communities and the environmental factors that structure them, deep-coverage small subunit (SSU) ribosomal RNA (rDNA) amplicon sequencing, community domain-specific quantitative PCR and physicochemical analyses were performed on samples collected along depth profiles. The analyses showed that the lakes harbored multiple and diverse prokaryotic communities whose distribution mirrored the water stratification patterns. Ursu Lake was found to be dominated by Bacteria and to have a greater prokaryotic diversity than Fara Fund Lake that harbored an increased cell density and was populated mostly by Archaea within oxic strata. In spite of their contrasting diversity, the microbial populations indigenous to each lake pointed to similar physiological functions within carbon degradation and sulfate reduction. Furthermore, the taxonomy results coupled with methane detection and its stable C isotope composition indicated the presence of a yet-undescribed methanogenic group in the lakes'' hypersaline monimolimnion. In addition, ultrasmall uncultivated archaeal lineages were detected in the chemocline of Fara Fund Lake, where the recently proposed Nanohaloarchaeota phylum was found to thrive.     

Campylobacterota dominate the microbial communities in a tropical karst subterranean estuary,with implications for cycling and export of nitrogen to coastal waters

Subterranean estuaries (STEs), the zones in which seawater and subsurface groundwater mix, are recognized as hotspots for biogeochemical reactions; however, little is known of the microbial communities that control many of those reactions. This study investigated the potential functions of microbes inhabiting a cenote and an offshore submarine spring (Pargos) in the near-coastal waters of the Yucatan Peninsula, Mexico. The inland cenote (Cenote Siete Bocas; C7B) is characterized by a chemocline that is host to an array of physicochemical gradients associated with microbial activities. The chemocline includes an increasing gradient in sulfide concentrations with depth and a decreasing gradient in nitrate concentrations. The microbial community within the chemocline was dominated by Sulfurimonas and Sulfurovum of the Campylobacteria, which are likely responsible for sulfide oxidation coupled with nitrate reduction. Although C7B has not been directly connected with Pargos Spring, water discharging from the spring has physicochemical characteristics and microbial community structures similar to C7B, strongly suggesting biogeochemical processing in the STE impacts groundwater composition prior to discharge. This work yields insight into the microbial communities and biogeochemical reactions in STEs in karstic aquifers and provides evidence for the importance of Campylobacteria in controlling nitrate concentrations exported to marine springs.