Bacterial Divisions Research Articles

Characterization of harmful gases and bioaerosols of pig farms: a review of the existing literature

From the ecological and economic point of view, intensive pig farming is drawing more and more attention due to the appearance of harmful substances, which significantly increases the risks of air, water and soil pollution. In addition, the optimal criteria for the content of harmful gases, dust and microorganisms in the environment of pig farms are currently not clearly defined. In order to better understand the interaction of harmful emissions and aerosols, the article reviews data from the literature on their main components, concentrations, and interactions. The results showed that the main pollutants in pig farming are harmful gases (ammonia (NH3), carbon dioxide (CO2), methane (CH4), nitrogen oxide (N2O), hydrogen sulfide (H2S), which are released from manure. The presence of even small concentrations of harmful gases in farm air can cause respiratory and cardiovascular system disorders not only in animals, but also in humans. Along with harmful gases, it is important to control the emission of solid particles and dust from livestock premises, which can form aerosols. Microbial aerosols in pig houses contain bacteria, fungi, viruses, which mainly come from the animals themselves, manure or service personnel. The bioaerosol includes the Firmicutes and Bacteroidetes bacterial divisions and their derivatives. In addition, the content of potentially dangerous bacteria in the bioaerosol can reach up to 40 %. A major concern causes the presence of a large number of antibiotic-resistant microorganisms in the air of these farms (including MRSA). The existing strategies and methods to combat these problems are still imperfect and need to be refined. Currently, the interaction of harmful gases, dust, solid particles and microorganisms is not taken into account, which can increase the toxic effect of each other on the animal's body. Therefore, there is a need for a better understanding of these interactions in order to improve the strategy for improving the microclimate conditions by correcting the microbiota, finding and developing biological preparations that contain natural bacteria capable of neutralizing odors and disinfecting livestock premises.

Event-driven acquisition for content-enriched microscopy.

A common goal of fluorescence microscopy is to collect data on specific biological events. Yet, the event-specific content that can be collected from a sample is limited, especially for rare or stochastic processes. This is due in part to photobleaching and phototoxicity, which constrain imaging speed and duration. We developed an event-driven acquisition framework, in which neural-network-based recognition of specific biological events triggers real-time control in an instant structured illumination microscope. Our setup adapts acquisitions on-the-fly by switching between a slow imaging rate while detecting the onset of events and a fast imaging rate during their progression. Thus, we capture mitochondrial and bacterial divisions at imaging rates that match their dynamic timescales while extending overall imaging durations. Because event-driven acquisition allows the microscope to respond specifically to complex biological events, it acquires data enriched in relevant content.

Microbial Metabolites Target Histone Deacetylases to Trigger Vascular Inflammation in Sickle Cell Disease

The gut microbiota is a fundamental regulator of host immune responses. Our group previously demonstrated that the depletion of the gut microbiota by broad-spectrum antibiotics (ABX) prevented neutrophil aging (a type of circadian priming) and vaso-occlusion and prolonged survival in a mouse model for sickle cell disease (SCD) (Zhang, D et al. Nature 2015, 570(7570):528-532); the mechanisms involved, however, are as yet unknown. Diverse metabolites are generated by the microbiota from the fermentation of exogenous undigested dietary components and endogenous substrates secreted by the host. Complex carbohydrates are metabolized into short-chain fatty acids (SCFAs), while cholesterol derivatives from the liver are converted into secondary bile acids by intestinal bacteria. The major SCFA producers are Bacteroidetes (gram-negative) and Firmicutes (gram-positive) divisions, and dysbiosis of these bacterial divisions is found in both SCD humans and mice, (Lim, S et al. Am J Hematol 2018, 93(4):E91-E93). Herein, we investigate whether and how microbiota-derived metabolites modulate the dynamics of neutrophils in vaso-occlusive processes in SCD mice. First, to C57BL/6 (wild-type, WT) mice we administered either: 1) one of three main SCFAs, namely sodium butyrate (Na-B), sodium propionate (Na-P), or sodium acetate (Na-A); or 2) a combination of two main secondary bile acids, lithocholic and deoxycholic acids. The number of circulating neutrophils with an aged phenotype (i.e., Ly6Ghi CD11bhi CD62Llo CXCR4pos, Casanova-Acebes, M et al. Cell 2013, 153(5):1025-1035) was assessed by flow cytometry over time. Numbers started to increase at 2h after Na-B administration and we observed a peak of accumulation of total and aged-like neutrophils at 4-5h, with a return to basal after 9h. Consistent with this finding, administration of Na-B to SCD mice led to augmented counts of aged-like neutrophils and impaired survival of mice subjected to inflammation. Interestingly, when SCD mice receiving prolonged ABX treatment (40-45 days) were also given daily Na-B for the last days of ABX treatment, the percentage of aged-like neutrophils in the circulation was higher than that found in the blood of SCD mice under ABX, but without Na-B (55% vs 24%), showing that Na-B by itself is able to reverse the reduction in neutrophil aging promoted by ABX. To address the impact of Na-B in SCD vaso-occlusion, intravital microscopy of the cremaster muscle of SCD mice, after inflammatory stimulus with TNFa, revealed that Na-B abrogated the beneficial effects of ABX and triggered vaso-occlusive processes. We found a 3-fold rise in the adhesion of leukocytes to the endothelium and a 2-fold slower blood flow rate in the microvasculature of mice who received Na-B (see Figure). These results support our hypothesis that the gut microbiota modulates inflammation and vaso-occlusion in SCD through the generation of SCFAs. Because Na-B is known to be a potent inhibitor of histone deacetylase (HDAC) enzymes, we induced HDAC inhibition in WT mice. Vorinostat, a potent synthetic HDAC inhibitor, led to a 3-fold greater expansion of total and aged-like neutrophils in the blood, suggesting a role for HDACs in neutrophil biology. Consistently, in vitro treatment of WT mouse neutrophils with vorinostat or Na-B accelerated the progressive acquisition of an aged-like phenotype, characterized by loss of L-selectin (CD62L). Proteome of neutrophils from WT mice after induction of circadian aging by anti-P and anti-E-selectin antibodies showed that aged neutrophils are similar to neutrophils from vorinostat-treated mice, with down-regulation of genes involved in mRNA processing, protein synthesis, and proteasome complex formation, suggesting that HDAC inhibition is the underlying mechanism driving neutrophil aging. Importantly, the down- and up-regulated pathways found in these neutrophils were the same as those found in SCD mouse neutrophils, and an opposite proteomic profile was observed in neutrophils from ABX-treated SCD mice. Our findings indicate that the intestinal microbiota drives vaso-occlusion and neutrophil aging in SCD mice through the production of metabolites that inhibit HDAC. They also define the microbiota as instigator and innate immunity as effector of vascular disease, such that targeting their crosstalk could be effective at alleviating the devastating symptoms in SCD patients. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Preprint Highlight: Event-driven acquisition for content-enriched microscopy.

Biological processes act over a broad range of temporal scales. Imaging fast-occurring and rare events would benefit from an on-the-fly adaptation of the acquisition frame rate according to the biological process' dynamics. This study presents an event-driven acquisition framework, where real-time machine-learning recognition of the onset of specific biological events triggers faster image acquisition. This framework was applied to follow mitochondrial fissions and bacterial divisions, achieving better temporal resolution during the events of interest along with minimized photo damage. Open code and a Micro-Manager plugin are provided, enabling adaptation to different microscopes and biological systems. The integration of real-time detection of precursors to specific events followed by tailored image acquisition will enable the enhanced characterization of fast and transient biological processes.

Event-driven acquisition for content-enriched microscopy.

A common goal of fluorescence microscopy is to collect data on specific biological events. Yet, the event-specific content that can be collected from a sample is limited, especially for rare or stochastic processes. This is due in part to photobleaching and phototoxicity, which constrain imaging speed and duration. We developed an event-driven acquisition framework, in which neural-network-based recognition of specific biological events triggers real-time control in an instant structured illumination microscope. Our setup adapts acquisitions on-the-fly by switching between a slow imaging rate while detecting the onset of events, and a fast imaging rate during their progression. Thus, we capture mitochondrial and bacterial divisions at imaging rates that match their dynamic timescales, while extending overall imaging durations. Because event-driven acquisition allows the microscope to respond specifically to complex biological events, it acquires data enriched in relevant content.

Phylogenomic analysis of the diversity of graspetides and proteins involved in their biosynthesis

BackgroundBacteria and archaea produce an enormous diversity of modified peptides that are involved in various forms of inter-microbial conflicts or communication. A vast class of such peptides are Ribosomally synthesized, Postranslationally modified Peptides (RiPPs), and a major group of RiPPs are graspetides, so named after ATP-grasp ligases that catalyze the formation of lactam and lactone linkages in these peptides. The diversity of graspetides, the multiple proteins encoded in the respective Biosynthetic Gene Clusters (BGCs) and their evolution have not been studied in full detail. In this work, we attempt a comprehensive analysis of the graspetide-encoding BGCs and report a variety of novel graspetide groups as well as ancillary proteins implicated in graspetide biosynthesis and expression.ResultsWe compiled a comprehensive, manually curated set of graspetides that includes 174 families including 115 new families with distinct patterns of amino acids implicated in macrocyclization and further modification, roughly tripling the known graspetide diversity. We derived signature motifs for the leader regions of graspetide precursors that could be used to facilitate graspetide prediction. Graspetide biosynthetic gene clusters and specific precursors were identified in bacterial divisions not previously known to encode RiPPs, in particular, the parasitic and symbiotic bacteria of the Candidate phyla radiation. We identified Bacteroides-specific biosynthetic gene clusters (BGC) that include remarkable diversity of graspetides encoded in the same loci which predicted to be modified by the same ATP-grasp ligase. We studied in details evolution of recently characterized chryseoviridin BGCs and showed that duplication and horizonal gene exchange both contribute to the diversification of the graspetides during evolution.ConclusionsWe demonstrate previously unsuspected diversity of graspetide sequences, even those associated with closely related ATP-grasp enzymes. Several previously unnoticed families of proteins associated with graspetide biosynthetic gene clusters are identified. The results of this work substantially expand the known diversity of RiPPs and can be harnessed to further advance approaches for their identification.

Effects of Xian-Ling-Gu-Bao capsule on the gut microbiota in ovariectomized rats: Metabolism and modulation

Xian-Ling-Gu-Bao capsule (XLGB) has been proven to prevent and treat osteoporosis. However, as a long-term oral formula, XLGB's effects on the metabolic capacity, structure and function of gut microbiota have yet to be elucidated in ovariectomized (OVX) rats. Our objectives were to evaluate the capacity of gut microbiota for metabolizing XLGB ingredients and to assess the effect of this prescription on gut microbiota. Herein, an integrated analysis that combined ultrahigh-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) and ultrahigh-performance liquid chromatography tandem triple quadrupole mass spectrometry (UPLC-TQD-MS) was conducted to determine the metabolic capacity of gut microbiota. The effects of XLGB on gut microbiota were explored by metagenomic sequencing in OVX rats. Fecal samples from each group were collected after intragastric administration for three months. In total, 64 biotransformation products were fully characterized with rat gut microbiota from the OVX group and the XLGB group. The deglycosylation reaction was the main biotransformation pathway in core structures in the group that was incubated with XLGB. Compared with the OVX group, different biotransformation products and pathways of the XLGB group after incubation for 2 h and 8 h were described. After three months of feeding with XLGB, the domesticated gut microbiota was conducive to the production of active absorbed components via deglycosylation, such as icaritin, psoralen and isopsoralen. Comparisons of the gut microbiota of the OVX and XLGB groups showed differences in the relative abundances of the two dominant bacterial divisions, namely, Firmicutes and Bacteroidetes. The proportion of Firmicutes was significantly lower and that of Bacteroidetes was significantly higher in the XLGB group. This result demonstrated that XLGB could provide a basis for the treatment of osteoporosis by regulating lipid and bile acid metabolism. In addition, the increase in Lactobacillus, Bacteroides and Prevotella could be an important factor that led to easier production of active absorbed aglycones in the XLGB group. Our observation provided further evidence of the importance of gut microbiota in the metabolism and potential activity of XLGB.

Molecular Characterization of Bacterial Community Composition in the Rhizosphere of Invasive Plant Species Amur Honeysuckle (<i>Lonicera maackii</i>) in an Urban Wetland Forest

The goal of this research was to determine the effects of the growth of invasive plant Amur Honeysuckle (Lonicera maackii) on the rhizosphere bacterial community composition, and diversity in an urban wetland forest ecosystem. Bacterial communities from the rhizosphere of 5 L. maackii plants and control bulk soils that did not have any L. maackii were investigated at Nina Mason Pulliam EcoLab (NMPE) using a culture-independent pipeline. Bacterial communities were characterized by PCR amplification and cloning 16S rRNA gene fragments following total DNA isolation from the soil samples. Microbial communities associated with both L. maackii rhizosphere and control sites showed high bacterial diversity within each site and taxa unique to individual sites were observed. Phylogenetic analyses revealed 80% of 400 16S rDNA clones were classified as α-, β- and γ-Proteobacteria, Acidobacteria, Actinobacteria, Cytophaga-Flexibacter-Bacteroides (CFB) group, and Verrucomicrobia. Members of the Proteobacteria and Acidobacterium represented 66.5% and 14.5% of the clone library, respectively, whereas the remaining bacterial divisions each comprised less than 7% of the clone library. Twenty-five 16S rDNA clones could not be classified into any known bacterial divisions. Statistical analyses showed significant differences in the presence of L. maackii on the proportions of 16S rDNA clones affiliated with Proteobacteria and Acidobacterium, suggesting bacterial community composition and structure does significantly change in the presence of L. maackii. However, sequence-based community analysis and the corresponding lack of intact microbial cultures limit understanding of the potential influences of enriched microbial taxa on plant hosts and their roles in ecosystem functioning.

Bacterial O-GlcNAcase genes abundance decreases in ulcerative colitis patients and its administration ameliorates colitis in mice

ObjectiveO-linked N-acetylglucosaminylation (O-GlcNAcylation), controlled by O-GlcNAcase (OGA) and O-GlcNAc transferase (OGT), is an important post-translational modification of eukaryotic proteins and plays an essential role in regulating gut inflammation. Gut microbiota...

From conservation to structure, studies of magnetosome associated cation diffusion facilitators (CDF) proteins in Proteobacteria.

Magnetotactic bacteria (MTB) are prokaryotes that sense the geomagnetic field lines to geolocate and navigate in aquatic sediments. They are polyphyletically distributed in several bacterial divisions but are mainly represented in the Proteobacteria. In this phylum, magnetotactic Deltaproteobacteria represent the most ancestral class of MTB. Like all MTB, they synthesize membrane-enclosed magnetic nanoparticles, called magnetosomes, for magnetic sensing. Magnetosome biogenesis is a complex process involving a specific set of genes that are conserved across MTB. Two of the most conserved genes are mamB and mamM, that encode for the magnetosome-associated proteins and are homologous to the cation diffusion facilitator (CDF) protein family. In magnetotactic Alphaproteobacteria MTB species, MamB and MamM proteins have been well characterized and play a central role in iron-transport required for biomineralization. However, their structural conservation and their role in more ancestral groups of MTB like the Deltaproteobacteria have not been established. Here we studied magnetite cluster MamB and MamM cytosolic C-terminal domain (CTD) structures from a phylogenetically distant magnetotactic Deltaproteobacteria species represented by BW-1 strain, which has the unique ability to biomineralize magnetite and greigite. We characterized them in solution, analyzed their crystal structures and compared them to those characterized in Alphaproteobacteria MTB species. We showed that despite the high phylogenetic distance, MamBBW-1 and MamMBW-1 CTDs share high structural similarity with known CDF-CTDs and will probably share a common function with the Alphaproteobacteria MamB and MamM.

Epiphytic bacterial community composition on the surface of the submerged macrophyte Myriophyllum spicatum in a low-salinity sea area of Hangzhou Bay

Abstract In this study, we conducted a comparative analysis of the abundance and diversity of bacteria on the surface of the submerged macrophyte Myriophyllum spicatum, as well as in the surrounding water column and sediment in the low-salinity area of Hangzhou Bay, China. Bacterial clones from three clone libraries were classified into 2089 operational taxonomic units (OTUs), most of which affiliated with bacterial divisions commonly found in marine ecosystems. Alphaproteobacteria, Cyanobacteria and Gammaproteobacteria were the most abundant groups of bacteria on the surface of plants, in the water column and sediment, respectively. Epiphytic bacterial communities were more closely related to those in the sediment than bacterioplankton, and some species of epiphytic bacteria were found only on the surface of M. spicatum. The relative abundance of epiphytic bacterial genera associated with breakdown of organic compounds and with cellulose digestion was higher in October than that in July. These results suggested that bacterial communities on the surface of M. spicatum may originate from sediment bacterial communities and their specific structure was gradually formed on the surface of M. spicatum after being cultivated in low-salinity seawater.

Life in Hot Spring Microbial Mats Located in the Trans-Mexican Volcanic Belt: A 16S/18S rRNA Gene and Metagenomic Analysis

ABSTRACTThe geothermal system of the Araró region, located in the Trans-Mexican Volcanic Belt of México, hosts various hot springs with unique physicochemical characteristics, including temperatures ranging from 45°C to 78°C. The microbial diversity in these hot springs has been explored only by culture-dependent surveys. In this study, we performed metagenomic Illumina MiSeq, and 16S and 18S rRNA pyrosequencing analysis of the microbial life are residing in the microbial mats of the springs called “Tina–Bonita”. Our results show the presence of 186 operational taxonomic units, 99.7% of which belong to bacteria, 0.27% to eukaryotes, and 0.03% to archaea. The most abundant bacterial divisions are the Proteobacteria, Chloroflexi, and Cyanobacteria, which include 105 genera. The ecological indexes indicate that the microbial mats have moderate microbial diversity. An abundant group of genes that participate in photosynthesis, including photosynthetic electron transport, as well as photosystems I and II, were detected. Another cluster of genes was found that participates in sulfur, nitrogen, and methane metabolism. Finally, this phylogenetic and metagenomic analysis revealed an unexpected taxonomic and genetic diversity, expanding our knowledge of microbial life under specific extreme conditions.

Strigolactones cross the kingdoms: plants, fungi, and bacteria in the arbuscular mycorrhizal symbiosis.

Strigolactones (SLs) first evolved as regulators of simple developmental processes in very ancient plant lineages, and then assumed new roles to sustain the increasing biological complexity of land plants. Their versatility is also shown by the fact that during evolution they have been exploited, once released in the rhizosphere, as a communication system towards plant-interacting organisms even belonging to different kingdoms. Here, we reviewed the impact of SLs on soil microbes, paying particular attention to arbuscular mycorrhizal fungi (AMF). SLs induce several responses in AMF, including spore germination, hyphal branching, mitochondrial metabolism, transcriptional reprogramming, and production of chitin oligosaccharides which, in turn, stimulate early symbiotic responses in the host plant. In the specific case study of the AMF Gigaspora margarita, SLs are also perceived, directly or indirectly, by the well-characterized population of endobacteria, with an increase of bacterial divisions and the activation of specific transcriptional responses. The dynamics of SLs during AM root colonization were also surveyed. Although not essential for the establishment of this mutualistic association, SLs act as positive regulators as they are relevant to achieve the full extent of colonization. This possibly occurs through a complex crosstalk with other hormones such as auxin, abscisic acid, and gibberellins.

Integrated microfluidic platform for rapid antimicrobial susceptibility testing and bacterial growth analysis using bead-based biosensor via fluorescence imaging

The paper describes a droplet-based microfluidic method for phenotypic-based antimicrobial susceptibility testing (AST). In particular, this micro-droplet-based phenotypic assay evaluates susceptibility of different bacterial strains towards antibiotics by tracking effects on individual bacterial cells, including changes in bacterial cell number and morphology. The platform was validated by applying the method to test the responses of E. coli ATCC 25922 and 6937 (a clinical isolate), in spiked urine samples at a concentration of 5 × 104 cfu mL−1, to the antibiotics ceftazidime and levofloxacin. Both E. coli strains showed dose-dependent inhibition of bacterial replication and morphological alteration. These correlated well with minimal inhibitory concentrations determined by the reference broth microdilution method. Discrete bacterial divisions and morphological changes were observed within 20 min of on-chip incubation, demonstrating performance of rapid AST directly on urine samples. As proof-of-concept, specific bead-based biosensors were tested for capture and detection of E. coli for on-bead proliferation. The method has the attractive feature of allowing the detection of at least one bacterium per bead in less than 30 min. It can potentially be used to isolate a specific bacterial strain directly from patient urine samples for AST monitoring.

Engineered bacteria detect gut inflammation in mice

A new strain of engineered bacteria can detect inflammation in the colon of mice even after more than 1,000 bacterial divisions, researchers report (Nat. Biotechnol. 2017, DOI: 10.1038/nbt.3879). Such a microbe could help doctors diagnose and monitor diseases such as inflammatory bowel disease. Pamela A. Silver and coworkers at Harvard University engineered nonpathogenic Escherichia coli to detect and respond to tetrathionate, a transient product of a reactive oxygen species released by intestinal cells during inflammation. The researchers inserted two genetic circuits into the bacterial genome. The first circuit produces the transcriptional factor Cro in response to tetrathionate, and Cro triggers a second “memory” circuit to produce the protein β-galactosidase. Even when tetrathionate is no longer around, the bacteria “remember” the exposure and continue to produce both proteins. The researchers monitored inflammation in mice treated with the microbes by measuring β-galactosidase in the animals’ feces. ...

Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond.

Modern phototrophic microbial mats are complex communities often used as analogs of major Precambrian ecosystems. Characterizing biotic, notably metabolic, interactions among different microbial mat members is essential to gain insights into the ecology and biogeochemistry of these systems. We applied 16S/18S rRNA metabarcoding approaches to characterize the structure of archaea, bacteria and protist communities from microbial mats collected along strong physicochemical (oxygen, salinity, temperature, depth) gradients in a shallow pond at the salar de Llamara (Chile). All mats were highly diverse, including members of virtually all known high-rank eukaryotic and prokaryotic taxa but also many novel lineages. Bacterial candidate divisions accounted for almost 50% of sequences in deeper mats, while Archaea represented up to 40% of sequences in some mat layers. Molecular phylogenetic analyses revealed six novel deeply divergent archaeal groups, along abundant and diverse Pacearchaeota and Woesearchaeota. Multivariate statistical analyses showed that local environmental conditions strongly influenced community composition. Co-occurrence network structure was markedly different between surface mats located in the oxygenated zone and mats located in transition and anoxic water layers. We identified potential biotic interactions between various high- and low-rank taxa. Notably, a strong positive correlation was observed between Lokiarchaeota and the poorly known candidate bacterial division TA06.

Spatiotemporal variation of bacterial and archaeal communities in a pilot-scale constructed wetland for surface water treatment

Microorganisms play important roles in the reduction of organic and inorganic pollutants in constructed wetlands used for the treatment of polluted surface water. However, the diversity and structure of microbial community in surface water constructed wetland system remain poorly known. The present study was made to characterize bacterial and archaeal communities in a surface water constructed wetland using Illumina high-throughput sequencing. The diversity and structure of both bacterial and archaeal communities illustrated a remarkable spatiotemporal variation. Archaeal communities showed lower richness and diversity than bacterial communities. Bacterial diversity decreased with increasing wetland layer depth. A variety of bacterial phyla or candidate divisions were found in wetland bacterial communities, including Proteobacteria, Chloroflexi, Firmicutes, Acidobacteria, Bacteroidetes, Nitrospirae, Actinobacteria, Spirochaetae, Planctomycetes, Chlorobi, Deferribacteres, Cyanobacteria, OP8, WS3, TA06, and OP11, while Proteobacteria, Chloroflexi, and Firmicutes were the major bacterial groups. Euryarchaeota and Thaumarchaeota dominated wetland archaeal communities.

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.

Illuminating microbial dark matter in meromictic Sakinaw Lake.

Despite recent advances in metagenomic and single-cell genomic sequencing to investigate uncultivated microbial diversity and metabolic potential, fundamental questions related to population structure, interactions, and biogeochemical roles of candidate divisions remain. Numerous molecular surveys suggest that stratified ecosystems manifesting anoxic, sulfidic, and/or methane-rich conditions are enriched in these enigmatic microbes. Here we describe diversity, abundance, and cooccurrence patterns of uncultivated microbial communities inhabiting the permanently stratified waters of meromictic Sakinaw Lake, British Columbia, Canada, using 454 sequencing of the small-subunit rRNA gene with three-domain resolution. Operational taxonomic units (OTUs) were affiliated with 64 phyla, including more than 25 candidate divisions. Pronounced trends in community structure were observed for all three domains with eukaryotic sequences vanishing almost completely below the mixolimnion, followed by a rapid and sustained increase in methanogen-affiliated (∼10%) and unassigned (∼60%) archaeal sequences as well as bacterial OTUs affiliated with Chloroflexi (∼22%) and candidate divisions (∼28%). Network analysis revealed highly correlated, depth-dependent cooccurrence patterns between Chloroflexi, candidate divisions WWE1, OP9/JS1, OP8, and OD1, methanogens, and unassigned archaeal OTUs indicating niche partitioning and putative syntrophic growth modes. Indeed, pathway reconstruction using recently published Sakinaw Lake single-cell genomes affiliated with OP9/JS1 and OP8 revealed complete coverage of the Wood-Ljungdahl pathway with potential to drive syntrophic acetate oxidation to hydrogen and carbon dioxide under methanogenic conditions. Taken together, these observations point to previously unrecognized syntrophic networks in meromictic lake ecosystems with the potential to inform design and operation of anaerobic methanogenic bioreactors.

Higher blood glucose level associated with body mass index and gut microbiota in elderly people.

BackgroundSome dominant bacterial divisions of the intestines have been linked to metabolic diseases such as overweight and diabetes.ObjectiveA pilot study aimed to evaluate the relations between the culturable intestinal bacteria with body mass index (BMI) and some principal cellular and metabolic markers of blood in people older than 65.DesignAltogether 38 generally healthy elderly people were recruited: ambulatory (n=19) and orthopedic surgery (n=19). Questionnaires on general health, anthropometric measurements, routine clinical and laboratory data, and quantitative composition of cultivable gut microbiota were performed.ResultsBlood glucose level was positively correlated with BMI (r=0.402; p=0.014). Higher blood glucose level had negative correlation with relative share of intestinal anaerobic bacteria such as bacteroides (r=−0.434; p=0.0076) and gram-positive anaerobic cocci (r=−0.364; p=0.027). In contrast, the relative share of bifidobacteria (r=0.383; p=0.019) and staphylococci (r=0.433; p=0.008) was positively correlated to blood glucose level. In elderly people, a higher blood glucose concentration was predicted by the reduction of the anaerobes’ proportion (adj. sex, age, and BMI R2=0.192, p=0.028) and that of Bacteroides sp. (adj. R2=0.309, p=0.016).ConclusionA tight interplay between increased BMI, level of blood glucose, and the reduced proportion of cultivable bacteroides is taking place in the gut microbiota of elderly people.