Nitrogen removal and microbial communities in a three-stage system simulating a riparian environment

The riparian zone is an active interface for nitrogen removal, in which nitrogen transformations by microorganisms have not been valued. In this study, a three-stage system was constructed to simulate the riparian zone environments, and nitrogen removal as well as the microbial community was investigated in this ‘engineered riparian system’. The results demonstrated that stage 1 of this system accounted for 41–51 % of total nitrogen removal. Initial ammonium loading and redox potential significantly impacted the nitrogen removal performances. Stages 1 and 2 were both composed of an anoxic/oxic (A/O) zone and an anaerobic column. The A/O zone removed most of the ammonium load (6.8 g/m²/day), while the anaerobic column showed a significant nitrate removal rate (11.1 g/m²/day). Molecular biological analysis demonstrated that bacterial diversity was high in the A/O zones, where ammonium-oxidizing bacteria and nitrite-oxidizing bacteria accounted for 8.42 and 3.32 % of the bacterial population, respectively. The denitrifying bacteria Acidovorax sp. and the nitrifying bacteria Nitrosospira/Nitrosomonas were the predominant microorganisms in this engineered riparian system. This three-stage system was established to achieve favorable nitrogen removal and the microbial community in the system was also retained. This investigation should deepen our understanding of biological nitrogen removal in engineered riparian zones.     

Blooms of single bacterial species in a coastal lagoon of the southwestern Atlantic Ocean

We investigated seasonal differences in community structure and activity (leucine incorporation) of the planktonic bacterial assemblage in the freshwater and brackish-water zones of a shallow coastal lagoon of the southwestern Atlantic Ocean. Alphaproteobacteria formed the dominant microbial group in both zones throughout the sampling period. After an intrusion of marine water, members of the SAR11 lineage became abundant in the brackish-water zone. These bacteria were apparently distributed over the lagoon during the following months until they constituted almost 30% of all prokaryotic cells at both sampling sites. At the first sampling date (March 2003) a single alphaproteobacterial species unrelated to SAR11, Sphingomonas echinoides, dominated the microbial assemblages in both zones of the lagoon concomitantly with a bloom of filamentous cyanobacteria. Pronounced maxima of leucine incorporation were observed once in each zone of the lagoon. In the freshwater zone, this highly active microbial assemblage was a mix of the typical bacteria lineages expected in aquatic systems. By contrast, a single bacterial genotype with >99% similarity to the facultative pathogen gammaproteobacterial species Stenotrophomonas maltophilia formed >90% of the bacterial assemblage (>10(7) cell ml(-1)) in the brackish-water zone at the time point of highest bacterial leucine incorporation. Moreover, these bacteria were equally dominant, albeit less active, in the freshwater zone. Thus, the pelagic zone of the studied lagoon harbored repeated short-term blooms of single bacterial species. This finding may have consequences for environmental protection.     

Molecular identification of diazotroph microbial consortia in mountain soil

Nitrogen fixing microbial consortia from soil samples taken from five altitudinal vegetation zones (alpine, subalpine, coniferous, beech, Maleia flood plain) of Parang Massif, Romania, were isolated and identified. Molecular characterisation of nitrogen fixing consortia was carried out by PCR and nested PCR with 7 primer sets specific to nifH genes. All nifH genes are specific to nitrogen fixation and are found within phylogenetically related organisms which have the nitrogenase enzyme complex. These molecular studies allowed the assessment of nifH gene diversity within these nitrogen fixing microbial consortia from different type of soils. At high altitude, a consortium of nitrogen fixing bacteria dominated by Azotobacter chroococcum and Azospirillum brasilense was found. Clostridium, Rhizobiales, Herbaspirillum, Frankia species were also found in different rations depending on the altitudinal vegetation zone.     

Soil microbes of an urban remnant riparian zone have greater potential for N removal than a degraded riparian zone

Soils in the riparian zone, the interface between terrestrial and aquatic ecosystems, may decrease anthropogenic nitrogen (N) loads to streams through microbial transformations (e.g., denitrification). However, the ecological functioning of riparian zones is often compromised due to degraded conditions (e.g., vegetation clearing). Here we compare the efficacy of an urban remnant and a cleared riparian zone for supporting a putative denitrifying microbial community using 16S rRNA sequencing and quantitative polymerase chain reaction of archaeal and bacterial nitrogen cycling genes. Although we had no direct measure of denitrification rates, we found clear patterns in the microbial communities between the sites. Greater abundance of N-cycling genes was predicted by greater soil ammonium (N-NH₄), organic phosphorus, and C:N. At the remnant site, we found positive correlations between microbial community composition, which was dominated by putative N oxidisers (Nitrosomonadaceae, Nitrospiraceae and Nitrosotaleaceae), and abundance of ammonia-oxidizing archaea (AOA), nirS, nirK and nosZ, whereas the cleared site had lower abundance of N-oxidisers and N cycling genes. These results were especially profound for the remnant riparian fringe, which suggests that this region maintains suitable soil conditions (via diverse vegetation structure and periodic saturation) to support putative N cyclers, which could amount to higher potential for N removal.     

Blooms of Single Bacterial Species in a Coastal Lagoon of the Southwestern Atlantic Ocean

We investigated seasonal differences in community structure and activity (leucine incorporation) of the planktonic bacterial assemblage in the freshwater and brackish-water zones of a shallow coastal lagoon of the southwestern Atlantic Ocean. Alphaproteobacteria formed the dominant microbial group in both zones throughout the sampling period. After an intrusion of marine water, members of the SAR11 lineage became abundant in the brackish-water zone. These bacteria were apparently distributed over the lagoon during the following months until they constituted almost 30% of all prokaryotic cells at both sampling sites. At the first sampling date (March 2003) a single alphaproteobacterial species unrelated to SAR11, Sphingomonas echinoides, dominated the microbial assemblages in both zones of the lagoon concomitantly with a bloom of filamentous cyanobacteria. Pronounced maxima of leucine incorporation were observed once in each zone of the lagoon. In the freshwater zone, this highly active microbial assemblage was a mix of the typical bacteria lineages expected in aquatic systems. By contrast, a single bacterial genotype with >99% similarity to the facultative pathogen gammaproteobacterial species Stenotrophomonas maltophilia formed >90% of the bacterial assemblage (>10⁷ cell ml⁻¹) in the brackish-water zone at the time point of highest bacterial leucine incorporation. Moreover, these bacteria were equally dominant, albeit less active, in the freshwater zone. Thus, the pelagic zone of the studied lagoon harbored repeated short-term blooms of single bacterial species. This finding may have consequences for environmental protection.     

Seasonal dynamics of akinetes of Anabaena flos-aquae in the bottom sediments and water column of a small Siberian reservoir

Seasonal dynamics of akinetes of Anabaena flos-aquae (Lyngb.) Breb. was studied in the sediments and the water column in profundal and littoral zones of a small Siberian reservoir. It was hypothesized that even in a shallow mixed reservoir cyanobacterial bloom initiates in the littoral zone and only then distributes throughout the water body. Two types of akinetes have been recognized: one type ensures vegetative reproduction, and the other, survival during adverse growth conditions. Seasonal dynamics of abundance of akinetes and vegetative cells was quite the same in water column in the littoral and profundal zones. However, there were differences in the seasonal dynamics of abundance of akinetes in the bottom sediments of these two areas: in the central zone the abundance increased throughout the vegetation period, whereas in the littoral zone the abundance decreased after settling of akinetes. During winter, the abundance of akinetes decreased in the sediments in both profundal and littoral zones. The explanation to this fact has not been found yet.     

Effects of Antarctic sea ice biota on seeding as studied in aquarium experiments

Summary The potential seeding impact of sea ice microbial communities was studied during late austral winter early spring 1988 in the Weddell Sea, Antarctica. Experiments were performed in seawater aquariums with natural seawater and seawater enriched with crushed ice. Algal, protozoan and bacterial cell numbers were followed, as well as nutrients and DOC levels. The results showed a potential seeding effect of sea ice communities to the water column. However, the type of ice communities differed greatly from each other and the effect of such seeding will be patchy. In our experiments seeding of seawater by ice rich in algae, flagellates and/or particulate organic carbon lead to the development of communities dominated either by diatoms or bacteria.Data presented here were collected during the European Polarstern Study (EPOS) sponsored by the European Science Foundation     

Microbial population structure in a stratified,acidic pit lake in the Iberian Pyrite Belt

Abstract

We examined the geochemistry and bacterial and archaeal community structure in the acidic (pH < 2.4) pit lake at Peña de Hierro, near the headwaters of the Río Tinto. The lake has strong vertical gradients in light, O₂, pH, conductivity, and dissolved ions. Bacterial and archaeal communities between 0 and 32?m displayed low species richness and evenness. Relatives of iron cycling taxa accounted for 60-90% of the operational taxonomic units (OTUs) throughout the water column. Relatives of heterotrophic, facultative Fe(III)-reducing species made up more than a third of the bacterial and archaeal community in the photic zone. Taxa related to Fe(II) oxidizers Ferrithrix thermotolerans and Acidithix ferrooxidans were also abundant in the photic zone. Below the photic zone, relatives of the lithoautotrophic Fe(II) oxidizers Leptospirillum ferrooxidans and Ferrovum myxofaciens bloomed at different depths within or just below the oxycline. Thermoplasmatales predominated in the deep, microoxic zone of the lake. The microbial population structure of the lake appears to be influenced by the production of oxygen and organic matter by phototrophs in a narrow zone at the lake surface and by strong geochemical gradients present in the water column that create distinct niches for separate Fe(II) oxidizers.     

Detection of microbial biomass by intact polar membrane lipid analysis in the water column and surface sediments of the Black Sea

The stratified water column of the Black Sea produces a vertical succession of redox zones, stimulating microbial activity at the interfaces. Our study of intact polar membrane lipids (IPLs) in suspended particulate matter and sediments highlights their potential as biomarkers for assessing the taxonomic composition of live microbial biomass. Intact polar membrane lipids in oxic waters above the chemocline represent contributions of bacterial and eukaryotic photosynthetic algae, while anoxygenic phototrophic bacteria and sulfate-reducing bacteria comprise a substantial amount of microbial biomass in deeper suboxic and anoxic layers. Intact polar membrane lipids such as betaine lipids and glycosidic ceramides suggest unspecified anaerobic bacteria in the anoxic zone. Distributions of polar head groups and core lipids show planktonic archaea below the oxic zone; methanotrophic archaea are only a minor fraction of archaeal biomass in the anoxic zone, contrasting previous observations based on the apolar derivatives of archaeal lipids. Sediments contain algal and bacterial IPLs from the water column, but transport to the sediment is selective; bacterial and archaeal IPLs are also produced within the sediments. Intact polar membrane lipid distributions in the Black Sea are stratified in accordance with geochemical profiles and provide information on vertical successions of major microbial groups contributing to suspended biomass. This study vastly extends our knowledge of the distribution of complex microbial lipids in the ocean.     

Responses of microbial activity in hyporheic pore water to biogeochemical changes in a drying headwater stream

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Unique Microbial Communities Inhabiting Underground Seawater in an Intertidal Area Utilized for Industrialized Aquaculture,as Compared with the Coastal Water

In recent decades, the decline of coastal water quality has promoted the birth of a new industrialized aquaculture mode in China, which involves the cultivation of organisms using underground seawater extracted from various depths below the intertidal zone. In view of the special physicochemical characteristics of underground seawater, the microbial community in this environment has attracted interest. In this study, the microbial community in the underground seawater of an intertidal area of the Qingdao coast of China was investigated. Compared with the upper coastal water, the underground seawater displayed lower numbers of microorganisms (2.7?±?0.3?×?10⁵ cells mL^?1 in underground seawater vs. 5.3?±?0.4?×?10⁵ cells mL^?1 in upper coastal seawater) but displayed much higher microbial diversity. At the phyla level, Proteobacteria, Bacteroidetes, Cyanobacteria, and Actinobacteria inhabited both environments, whereas bacteria in the phyla Planctomycetes, Deferribacteres, and Nitrospirae were recovered only from the underground seawater. Eighty-nine percent of the OTUs in the underground seawater were environmental specific. Furthermore, compared with coastal water, underground seawater displayed significant lower (p?<?0.05) concentration of NH₃-N, NO₂-N, PO₄-P, and DOC-C, and contained fewer potentially harmful pathogens (e.g., Verrucomicrobia/Opitutae) and more denitrifying bacteria (e.g., Shewanella denitrificans), thus making it more suitable for aquaculture.     

Microbial communities and diazotrophic activity differ in the root‐zone of Alamo and Dacotah switchgrass feedstocks

Nitrogen (N) bioavailability is a primary limiting nutrient for crop and feedstock productivity. Associative nitrogen fixation (ANF) by diazotrophic bacteria in root‐zone soil microbial communities have been shown to provide significant amounts of N to some tropical grasses, but this potential in switchgrass, a warm‐season, temperate, US native, perennial tallgrass has not been widely studied. ‘Alamo’ and ‘Dacotah’ are cultivars of switchgrass, adapted to the southern and northern regions of the United States, respectively, and offer an opportunity to better describe this plant–bacterial association. The nitrogenase enzyme activity, microbial communities, and amino acid profiles in the root‐zones of the two ecotypes were studied at three different plant growth stages. Differences in the nitrogenase enzyme activity and free soluble amino acid profiles indicated the potential for greater nitrogen fixation in the high productivity Alamo compared with the lower productivity Dacotah. Changes in the amino acid profiles and microbial community structure (rRNA genes) of the root‐zone suggest different plant–bacterial interactions can help to explain differences in nitrogenase activity. PICRUSt analysis revealed functional differences, especially nitrogen metabolism, that supported ecotype differences in root‐zone nitrogenase enzyme activity. It is thought that the greater productivity of Alamo increased the belowground flow of carbon into roots and root‐zone habitats, which in turn support the high energy demands needed to support nitrogen fixation. Further research is thus needed to understand plant ecotype and cultivar trait differences that can be used to breed or genetically modify crop plants to support root‐zone associations with diazotrophs.     

Seasonal changes in the microbial population of the water column and sediments of the Ongagawa River,northern Kyushu,Japan

The total viable count, population density of Escherichia coli and coliform bacteria, and nitrogen in the microbiomass (microbiomass-N) in sediments were monitored monthly at 12 points in the Ongagawa River basin from June 2002 to May 2006. The measurement of the sediment microbiomass-N was used for evaluation of the sediment’s microbial population in the river ecosystem. An extraordinarily high population of E. coli was observed during the season when there was stagnant water in the basin, with a high population and an insufficient drain diffusion system, and, thus hydrological water control is indispensable to prevent rapid E. coli growth. Microbiomass-N in sediments showed a negative correlation or independent fluctuation in relation to the bacterial population in the water column of the river. Seasonal changes in extracted nitrogen (N) in river sediments did not show correspondence with microbiomass-N in sediments. The microbiomass-N in sediments changed independently of the bacterial population in the river water, indicating that the high population of bacteria in the water does not lead to a high microbial population in river sediments. Ordination of the microbial parameters by canonical correspondence analysis (CCA) showed that microbiomass-N in sediments was quite different from other parameters. Relatively higher H⁺ (lower pH), PO₄ ³⁻ concentration and dissolved oxygen (DO) were the determinant parameters of higher microbiomass-N in sediments. A relative microbial abundance between the water column and sediments as well as each of the microbial populations in the water column and sediments could be a quantitative parameter for evaluating the biochemical processes of stream water.     

Bacteriohopanepolyols along redox gradients in the Humboldt Current System off northern Chile

Marine oxygen minimum zones (OMZs) are characterized by the presence of subsurface suboxic or anoxic waters where diverse microbial processes are responsible for the removal of fixed nitrogen. OMZs have expanded over past decades and are expected to continue expanding in response to the changing climate. The implications for marine biogeochemistry, particularly nitrogen cycling, are uncertain. Cell membrane lipids (biomarkers), such as bacterial bacteriohopanepolyols (BHPs) and their degradation products (hopanoids), have distinctive structural attributes that convey information about their biological sources. Since the discovery of fossil hopanoids in ancient sediments, the study of BHPs has been of great biogeochemical interest due to their potential to serve as proxies for bacteria in the geological record. A stereoisomer of bacteriohopanetetrol (BHT), BHT II, has been previously identified in OMZ waters and has as been unequivocally identified in culture enrichments of anammox bacteria, a key group contributing to nitrogen loss in marine OMZs. We tested BHT II as a proxy for suboxia/anoxia and anammox bacteria in suspended organic matter across OMZ waters of the Humboldt Current System off northern Chile, as well as in surface and deeply buried sediments (125–150 ky). The BHT II ratio (BHT II/total BHT) increases as oxygen content decreases through the water column, consistent with previous results from Perú, the Cariaco Basin and the Arabian Sea, and in line with microbiological evidence indicating intense anammox activity in the Chilean OMZ. Notably, BHT II is transported from the water column to surface sediments, and preserved in deeply buried sediments, where the BHT II ratio correlates with changes in δ¹⁵N sediment values during glacial–interglacial transitions. This study suggests that BHT II offers a proxy for past changes in the relative importance of anammox, and fluctuations in nitrogen cycling in response to ocean redox changes through the geological record.     

Comparative microbial ecology study of the sediments and the water column of the Río Tinto, an extreme acidic environment

Due to its highly metalliferous waters and low pH, the Rio Tinto has shown its potential for modelling both acid mine drainage systems and biohydrometallurgical operations. Most geomicrobiological studies of these systems have focused on the oxic water column. A sequence-based approach in combination with in situ detection techniques enabled us to examine the composition and structure of the microbial communities associated with the suboxic and anoxic sediments along the river course and to compare them with the planktonic communities inhabiting the water column. The results obtained with the different approaches were consistent and revealed some major patterns: higher cell density and higher richness (75 vs. 48 operational taxonomic units) in the sediments than in the water column. The microbial communities were related but the river sediments appear to be enriched in certain populations, some of which have not previously been reported in the Rio Tinto basin. The differences detected between sampling stations along the river correlate with certain environmental parameters (e.g. iron concentration gradient). The biological and geochemical data show the importance of the sediments as representing a phase of particular high diversity, probably related to key metabolic processes within both the iron and the sulfur cycles.     

Microbial Biomass, Activity, and Community Structure of Water and Particulates Retrieved by Backflow from a Waterflood Injection Well

Oil field injection water was allowed to back flow from two wells at the Packard drill site in Los Angeles, Calif., and was sampled at various times to obtain information about the biomass, potential activity, and community structure of the microbiota in the reservoir formation and in the injection water. Biomass was greatest in water samples that came from the zone near the injection site and dropped off sharply in subsequent samples, which were assumed to come from zones farther away from the well. Samples obtained from near the well also had visible exopolysaccharide blankets, as seen in scanning electron microscopic preparations. In one of the wells that was sampled, rates of glucose or acetate incorporation into microbial lipids correlated with biomass; but in the other well, activities correlated with the sampling time (volume of water that back flowed). Transmission electron micrographs showed a diverse, gram-negative bacterial population in a variety of physiological states. The analysis of the phospholipid ester-linked fatty acid profiles of the samples revealed consistently large proportions of 18:1ω7c fatty acids, indicating the presence of many anaerobes, facultative organisms, or both. Proportions of cyclopropyl fatty acids and ratios of trans/cis monoenoic compounds increased with the volume of water that back flowed (analogous with the distance into the formation), while the ratio of unsaturated/saturated compounds decreased, possibly indicating higher levels of stress or starvation in the microbial communities farthest from the injection well. Greater than 90% of the total biomass was trapped on glass fiber filters, indicating that the microbiota were largely attached to particles or were clumped. These sampling techniques and analytical methods may prove useful in monitoring for problems with microbes (e.g., plugging) in waterflood operations and in the preparation of water injection wells for enhanced oil recovery by the use of microbes.     

A Simple Technique of Studying Water Deficit Effects on Nitrogen Fixation in Nodules without Influencing the Whole Plant

Cowpea (Vigna unguiculata L. Walp cv C-152) plants were grown in a system in which watering was withheld from the soil zone containing nodules, while the plants were able to maintain normal water status. The system was developed in a pot by making two soil zones, an upper and a lower separated by a gravel column between these two zones. Plants extended their roots into the lower layer of soil and were able to absorb water. The dry matter accumulation, photosynthesis rate, and leaf area development of the plant were not affected when the upper soil zone was dried, but the water potential of the nodules was lower than in the nodules in fully irrigated pots. Nitrogenase activity in the nodules obtained from plants stressed in the upper zone only was lower than in nodules obtained from fully irrigated plants. The present technique is helpful in distinguishing the direct water stress effects on nitrogen fixation compared to those mediated via photosynthate availability.     

Relative influences of submersed macrophytes and bioturbating fauna on biogeochemical processes and microbial activities in freshwater sediments

1. Invertebrates and aquatic plants often play a key role in biogeochemical processes occurring at the water–sediment interface of aquatic ecosystems. However, few studies have investigated the respective influences of plants and bioturbating animals on ecological processes (nutrient fluxes, benthic oxygen uptake, microbial activities) occurring in freshwater sediments. 2. We developed a laboratory experiment in aquaria to quantify the effects of (i) one invertebrate acting as a bioturbator (Tubifex tubifex); (ii) one submersed plant with a high sediment‐oxygenating potential (Myriophyllum spicatum) and (iii) one submersed plant with a low sediment‐oxygenating potential (Elodea canadensis). 3. The tubificid worms significantly increased the fluxes of nitrogen at the water–sediment interface (influx of nitrate, efflux of ammonium), whereas the two plant species did not have significant influences on these nitrogen fluxes. The differences in nitrogen fluxes between tubificid worms and plants were probably due to the bioirrigation process caused by T. tubifex, which increased water exchanges at the water–sediment interface. Tubifex tubifex and M. spicatum produced comparable reductions of nutrient concentrations in pore water and comparable stimulations of benthic oxygen uptake and microbial communities (percentages of active eubacteria and hydrolytic activity) whereas E. canadensis had a very weak influence on these variables. These differences between the two plants were due to their contrasting abilities to increase oxygen in sediments by radial oxygen losses (release of oxygen from roots). 4. Our study suggests that the bioirrigation process and radial oxygen loss are major functional traits affecting biogeochemical functioning at the water–sediment interface of wetlands.     

Co-occurrence of denitrification and nitrogen fixation in a meromictic lake, Lake Cadagno (Switzerland)

The nitrogen cycling of Lake Cadagno was investigated by using a combination of biogeochemical and molecular ecological techniques. In the upper oxic freshwater zone inorganic nitrogen concentrations were low (up to ～3.4 μM nitrate at the base of the oxic zone), while in the lower anoxic zone there were high concentrations of ammonium (up to 40 μM). Between these zones, a narrow zone was characterized by no measurable inorganic nitrogen, but high microbial biomass (up to 4 × 10⁷ cells ml^?1). Incubation experiments with ¹⁵N‐nitrite revealed nitrogen loss occurring in the chemocline through denitrification (～3 nM N h^?1). At the same depth, incubations experiments with ¹⁵N₂‐ and ¹³C_DIC‐labelled bicarbonate, indicated substantial N₂ fixation (31.7–42.1 pM h^?1) and inorganic carbon assimilation (40–85 nM h^?1). Catalysed reporter deposition fluorescence in situ hybridization (CARD‐FISH) and sequencing of 16S rRNA genes showed that the microbial community at the chemocline was dominated by the phototrophic green sulfur bacterium Chlorobium clathratiforme. Phylogenetic analyses of the nifH genes expressed as mRNA revealed a high diversity of N₂ fixers, with the highest expression levels right at the chemocline. The majority of N₂ fixers were related to Chlorobium tepidum/C. phaeobacteroides. By using Halogen In Situ Hybridization‐Secondary Ion Mass Spectroscopy (HISH‐SIMS), we could for the first time directly link Chlorobium to N₂ fixation in the environment. Moreover, our results show that N₂ fixation could partly compensate for the N loss and that both processes occur at the same locale at the same time as suggested for the ancient Ocean.     

Impact of paleoclimate on the distribution of microbial communities in the subsurface sediment of the Dead Sea

A long sedimentary core has been recently retrieved from the Dead Sea Basin (DSB) within the framework of the ICDP‐sponsored Dead Sea Deep Drilling Project. Contrasting climatic intervals were evident by distinctive lithological facies such as laminated aragonitic muds and evaporites. A geomicrobiological investigation was conducted in representative sediments of this core. To identify the microbial assemblages present in the sediments and their evolution with changing depositional environments through time, the diversity of the 16S rRNA gene was analyzed in gypsum, aragonitic laminae, and halite samples. The subsurface microbial community was largely dominated by the Euryarchaeota phylum (Archaea). Within the latter, Halobacteriaceae members were ubiquitous, probably favored by their ‘high salt‐in’ osmotic adaptation which also makes them one of the rare inhabitants of the modern Dead Sea. Bacterial community members were scarce, emphasizing that the ‘low salt‐in’ strategy is less suitable in this environment. Substantial differences in assemblages are observed between aragonitic sediments and gypsum–halite ones, independently of the depth and salinity. The aragonite sample, deposited during humid periods when the lake was stratified, consists mostly of the archaeal MSBL1 and bacterial KB1 Candidate Divisions. This consortium probably relies on compatible solutes supplied from the lake by halotolerant species present in these more favorable periods. In contrast, members of the Halobacteriaceae were the sole habitants of the gypsum–halite sediments which result from a holomictic lake. Although the biomass is low, these variations in the observed subsurface microbial populations appear to be controlled by biological conditions in the water column at the time of sedimentation, and subsequently by the presence or absence of stratification and dilution in the lake. As the latter are controlled by climatic changes, our data suggest a relationship between local lacustrine subsurface microbial assemblages and large‐scale climatic variations over the Dead Sea Basin.