Exploration of Microbial Diversity and Community Structure of Lonar Lake: The Only Hypersaline Meteorite Crater Lake within Basalt Rock

Sediment microbial communities of a technogenic saline-alkaline reservoir

Various natural saline and alkaline habitats have recently been widely investigated, but knowledge of anthropogenic habitats with more complex environmental conditions is still lacking. This research looks at the structure of microbial communities in 18 bottom sediment samples from a technogenic water body with saline and alkaline composition. The core samples were collected from 2 columns in the western and eastern parts of an artificial water body at the Verkhnekamskoe Salt Deposit (Russia). The microbial community structure was studied using high-throughput 16S rRNA gene sequencing. The bottom sediment composition (salinity, pH, and toxic element content) varies greatly with depth and laterally throughout the study area. The study found a considerable difference in bacterial community diversity between the 2 columns, but no considerable difference was found between the communities at various depths of the studied layers. Proteobacteria, Firmicutes, and Actinobacteria, which are common in both natural and artificial saline and alkaline environments, make up the majority of the bacteria found in the samples. Studies have shown that salinity and total alkalinity are the key factors influencing the formation of microbial communities. Ralstonia and Pseudomonas were the two most common genera in the sediment samples. These two genera are known for having high metabolic flexibility, which means they can survive in extreme environments and use a variety of carbon compounds as energy sources. The study also found that Ralstonia is indicator bacteria in samples with the highest concentrations of toxic elements compared to the other samples. A relatively high microbial diversity was discovered in the studied anthropogenic water reservoir despite the extreme alkaline and saline conditions, but it is considerably lower than that found in natural, less alkaline habitats. This research offers insight into the mechanisms behind microbial community formation in complex anthropogenic environments and covers key factors in microbial community distribution.

Synergistic impact of bioavailable PHEs and alkalinity on microbial diversity and traits in agricultural soil adjacent to chromium-asbestos mines

Soil microbial communities undergo constant fluctuations, particularly in response to environmental factors. Although the deposition of toxic mine waste is recognized for introducing potentially hazardous elements (PHEs) into the soil, its specific impacts on microbial communities remain unclear. This study aims to explore the combined effects of soil alkalinity and bioavailable PHEs on microbial diversity and traits in agricultural soil adjacent to a chromium-asbestos mining area. By employing a comprehensive analysis, this study indicated that microbiological attributes were reduced in contaminated areas (zone 1), whereas both the levels of bioavailable PHEs (CrWs: 31.08 mg/kg, NiWs: 13.90 mg/kg) and alkalinity indices (CROSS, MCAR, MH) were significantly higher. The spatial distribution of soil alkalinity and bioavailable PHEs, primarily originating from chromium-asbestos mines, has been determined. This study also elucidates the negative relationship between soil stressors (Alkalinity and PHEs) and microbial activities (soil enzymatic activity, microbial respiration, and biomass carbon). The vector's length exhibited a notable difference between zone 1 (0.51) and zone 2 (0.32), indicating a substantial limitation on carbon (C). Also, the investigation of soil bacterial diversity unveiled notable disparities in the prevalence of microbial populations inside zone 1. Proteobacteria constituted 57.18% of the total population indicating a noteworthy prevalence in the contaminated soils. Finally, the random forest (RF) algorithm from machine learning was selected and proven to be a robust choice in Taylor diagrams for predicting the causative stressors responsible for the deterioration of soil microbial health. Therefore, this research offers insights into the health and resilience of soil microbial communities under synergistic stress conditions, which will aid environmentalists in planning future interventions and improving sustainable farming techniques.

Effects of Fishery Utilization on the Physicochemical Index and Microbial Community Composition in Saline-Alkaline Water

Fishery utilization of idle saline-alkaline water resources offers various benefits including reducing surrounding soil salinity, improving the ecological environment, increasing arable land area, and providing economic advantages to the fishery industry. However, for decades, the characteristics and regulatory mechanisms of microbial communities that affect fishery utilization have not been clear, which restricts their application. In this study, high-throughput 16S rRNA amplicon sequencing was employed to analyze the bacterial community in these water resources. The sequencing yielded high-quality sequences (2,765,063), resulting in the identification of 18,761 bacterial operational taxonomic units (OTUs). Analysis revealed that the type of saline-alkaline water had a more significant influence on the bacterial community compared to seasonal variations within the aquaculture period. The Chao index for saline-alkaline ponds (ASW) was significantly lower (P < 0.05) than for still saline-alkaline water (SSW) and flowing saline-alkaline water (FSW), while the Shannon index for ASW was also significantly lower (P < 0.05) compared to FSW. When comparing ASW to nonaquaculture saline-alkaline water, a decrease in Proteobacteria to 26.87% was noted, particularly α-proteobacteria and γ-proteobacteria, accompanied by a rapid increase in Actinobacteria and Cyanobacteria to 28.60%. Networkx analysis further revealed that ASW significantly increased competition and amensalism from secondary saline-alkaline water microorganisms, resulting in a more solitary bacterial community composition as an adaptive strategy to cope with intense environmental pressures. Key bacterial species such as Pseudomonas, Hydrogenophaga, and Flavobacterium were found to be involved in hydrogen-cycling, nitrogen-cycling, and carbon-cycling, respectively, with all three exhibiting high abundance in FSW. Consequently, FSW demonstrates significant advantages in biogeochemical cycling, pollutant degradation, and the utilization of indigenous probiotic bacteria. Although the surface of abandoned secondary saline-alkaline land was covered with white salt particles, the fishery utilization of saline-alkaline water with low salinity levels (4.0-5.5), and the presence of nitrate and phosphate were identified as primary determinants of bacterial community composition. Nevertheless, a comparison of coastal high-salinity ponds indicated that salinity still selectively affects bacterial communities to some extent. Overall, our study provides valuable insights into the microbial regulation of nitrite during saline-alkaline water aquaculture, thereby aiding in the efficient utilization of secondary saline-alkaline water resources for fisheries.

Elucidating the synergistic effect of acidity and metalloid poisoning on the microbiome through metagenomics and machine learning approaches

The abundance and diversity of the microflora in a complex environment such as soil is everchanging. Mica mining has led to metalloid poisoning and changes in soil biogeochemistry affecting the overall produce and leading to toxic dietary exposure. The study focuses on two prominent stressors acidity and arsenic, in mining-contaminated agricultural locations. Soil samples were collected from agricultural fields at a distance of 50 m (zone 1) and 500 m (zone 2) from active mines. Mean arsenic concentration was higher in zone 1 and pH was lower. Geostatistical and self-organizing maps were employed to report that the pattern of localization of soil acidity and arsenic content is similar indicating a causal relationship. Cluster and principal component analysis were further used to materialize a negative effect of soil acidity fractions and arsenic labile pool on soil enzymatic activity (fluorescein diacetate, dehydrogenase, β-1,4-glucosidase, phosphatase, and urease), respiration and Microbial biomass carbon. Soil metagenomic analysis revealed significant differences in the abundance of microbial populations with zone 1 (contaminated zone) having lower alpha and beta diversity. Finally, the efficacy of several machine-learning tools was tested using Taylor diagrams and an effort was made to select a potent algorithm to predict the causal stressors responsible for depreciating soil microbial health. Random Forrest had superior predictive power based on numerical evidence and was therefore chosen as the best-fitted model. The aforementioned insights into soil microbial health and sustenance in stressed conditions can be beneficial for predicting remedial strategies and practicing sustainable agriculture.

Impact of artificial mixing and oxygenation on bacteria in a water transfer reservoir: Community succession and the role in water quality improvement

Artificial mixing and oxygenation induced by water-lifting aerations (WLAs) have the potential to improve water quality in reservoirs. However, there is a limited understanding of the bacterial community composition, assembly, and mechanisms behind water quality improvement under the influence of WLAs, especially in a water transfer reservoir. Here, the dynamics and relationship between water quality, bacterial diversity, and composition during the pre-operation, in-operation, and post-operation stages of WLAs were analyzed using high-throughput sequencing technology to explore the effects of artificially regulated bacteria on water quality improvement. WLAs operation led to the elimination of water stratification, significant bottom oxygenation, and reduction in nutrient concentrations. In addition, the operation of WLAs significantly changed the bacterial community composition, with an increase in richness, negligible difference in diversity, and a significant increase in the abundance of species with pollutant degradation functions, resulting in a shift from stochastic to deterministic processes of the bacterial community assembly. As a result, enhancement of the dominant bacteria responsible for organic matter degradation and denitrification and suppression of the emergence of algae-related bacteria were observed during the WLAs operation, and the ecosystem stability improved. Multiple analyses indicated a direct correlation between artificial mixing and oxygenation; changes in the bacterial community; and the reduction of nitrogen, phosphorus, and permanganate index in the water column. This study provides novel insights into in situ water quality enhancement and a valuable reference for understanding bacterial change patterns under artificially intervened conditions in water transfer reservoirs.

Industrial and Pharmaceutical Applications of Microbial Diversity of Hypersaline Ecology from Lonar Soda Crater

The unidentified geochemical and physiochemical characteristics of Soda Lakes across the globe make it a novel reservoir and bring attention to scientific civic for its conceivable industrial and pharmaceutical applications. In India, in the Maharashtra state, Lonar Lake is a naturally created Soda Lake by a meteorite impact. Phylogenetic data from this lake explored a diverse array of microorganisms like haloalkaliphilic bacteria and Archaea. Previously reported studies postulated the major microbial communities present in this lake ecosystem are Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria. Furthermore, it also contains Bacteroidetes, Nitrospirae, and Verrucomicrobia. This lake is also rich in phytoplankton, with the predominant presence of the Spirulina plantensis. Unique microbial strains from Lonar Lake ecosystems have fascinated consideration as a source of biological molecules with medicinal, industrial, and biotechnological potential. Recent literature revealed the isolation of antibioticproducing bacteria and alkaline proteases-producing alkaliphilic bacterium, as well as novel species of rare methylotrophs, other bacterial strains involved in producing vital enzymes, and unique actinomycetes are also reported. It indicates that the novel bacterial assemblage not reached hitherto may exist in this modified and unique ecology. This comprehensive review provides information about microbial diversity and its industrial and pharmaceutical interests that exist in Lonar Lake, which could be the future source of bioactive enzymes, biosurfactants, and biofuel and also useful in bioremediation. Furthermore, the novel species of microorganisms isolated from Lonar Lake have applications in the biosynthesis of medicines like antibiotics, antivirals, antifungals, anti-inflammatory agents, and precursors for synthesising valuable products. Data consolidated in the present review will cater to the needs of emerging industrial sectors for their commercial and therapeutic applications.

Arsenic-Containing Medicine Treatment Disturbed the Human Intestinal Microbial Flora

Human intestinal microbiome plays vital role in maintaining intestinal homeostasis and interacting with xenobiotics. Few investigations have been conducted to understand the effect of arsenic-containing medicine exposure on gut microbiome. Most animal experiments are onerous in terms of time and resources and not in line with the international effort to reduce animal experiments. We explored the overall microbial flora by 16S rRNA genes analysis in fecal samples from acute promyelocytic leukemia (APL) patients treated with arsenic trioxide (ATO) plus all-trans retinoic acid (ATRA). Gut microbiomes were found to be overwhelmingly dominated by Firmicutes and Bacteroidetes after taking medicines containing arsenic in APL patients. The fecal microbiota composition of APL patients after treatment showed lower diversity and uniformity shown by the alpha diversity indices of Chao, Shannon, and Simpson. Gut microbiome operational taxonomic unit (OTU) numbers were associated with arsenic in the feces. We evaluated Bifidobacterium adolescentis and Lactobacillus mucosae to be a keystone in APL patients after treatment. Bacteroides at phylum or genus taxonomic levels were consistently affected after treatment. In the most common gut bacteria Bacteroides fragilis, arsenic resistance genes were significantly induced by arsenic exposure in anaerobic pure culture experiments. Without an animal model, without taking arsenicals passively, the results evidence that arsenic exposure by drug treatment is not only associated with alterations in intestinal microbiome development at the abundance and diversity level, but also induced arsenic biotransformation genes (ABGs) at the function levels which may even extend to arsenic-related health outcomes in APL.

First report on microplastics contamination in a meteorite impact Crater Lake from India

Microplastic pollution is a worldwide concern affecting all environmental matrices, including pristine lakes. Lentic lakes operate as a sink for microplastics (MPs), which interfere with a biogeochemical cycle and, therefore, deserve immediate attention. We present a comprehensive assessment of MPs contamination in the sediment and surface water of a geo-heritage site, Lonar lake (India). It is the third largest natural saltwater lake and only basaltic crater in the world formed by meteoric impact around 52,000 years ago. Mean MPs abundance in lakeshore sediment and surface water was 14.44 particles/kg and 2.66 particles/L, respectively. Small-sized MPs dominate the hypersaline region of the lake. Transparent and green fragments and filaments morphotypes were abundant. Most of the MPs in Lonar lake were secondary in origin. FTIR-ATR analysis revealed 16 types of polymers in the lake, of which polypropylene, polyvinyl chloride, polyethylene, high-density polyethylene, low-density polyethylene, polystyrene, and polyester were the most common. The overall pollution load index (PLI) for Lonar lake sediment and water was 1.39 and 2.58, respectively. Although all sampling stations had significant MPs pollution (PLI > 1), there was noticeable station-specific variability, which could be linked to anthropogenic activities. Irresponsible tourist behavior and religious activities, coupled with poor waste management are the leading causes of MPs contamination in the lake. The current work fills a gap in the investigation of MP pollution in a crater lake formed by a meteorite impact by being the first to provide a precise estimate of the MPs contamination in the Lonar lake.

Bacterial and archaeal communities within the alkaline soda Langaco Lake in the Qinghai-Tibet Plateau

Purpose

Langaco Lake (LGL) is a soda lake located at an altitude of 4548 m in the Qinghai-Tibet Plateau in China. LGL exhibits unique hydrochemical characteristics among soda lakes, but little is known about the microbial diversity of LGL and the microbial interactions with environmental factors.

Methods

The water samples were filtered using chemical-grade cellulose acetate membrane (pore size of 0.45 μm), and the hydrochemical characteristics were analyzed. Community DNA was extracted, and then high-throughput sequencing of 16S rRNA genes was conducted to evaluate the composition of the microbial community.

Results

The high-throughput sequencing of 16S rRNA genes revealed that the bacterial diversity in LGL consisted of 327 genera in 24 phyla (4871 operational taxonomic units (OTUs); Shannon index values of 5.20–6.07), with a significantly higher diversity than that of the Archaea (eight phyla and 29 genera comprising 1008 OTUs; Shannon index values of 2.98–3.30). The bacterial communities were dominated by Proteobacteria (relative abundances of 42.79–53.70%), followed by Bacteroidetes (11.13–15.18%), Planctomycetes (4.20–12.82%), Acidobacteria (5.91–9.50%), Actinobacteria (2.60–5.80%), and Verrucomicrobia (2.11–4.08%). Furthermore, the archaeal communities were dominated by Crenarchaeota (35.97–58.29%), Euryarchaeota (33.02–39.89%), and Woesearchaeota (6.50–21.57%). The dominant bacterial genus was Thiobacillus (8.92–16.78%), and its abundances were most strongly correlated with the total phosphorus (TP) content, pH value, CO32− concentration, and temperature. The most abundant archaeal genus was Methanoregula (21.40–28.29%), and its abundances were the most highly correlated with the total organic carbon (TOC) content, total salinity (TS), and K+ and Na+ concentrations.

Conclusions

The results of this study provide valuable insights for developing a more comprehensive understanding of microbial diversity in these unique carbonate alkaline environments, as well as a better understanding of the microbial resources on the Qinghai-Tibet Plateau.

Geoalkalibacter halelectricus SAP-1 sp. nov. possessing extracellular electron transfer and mineral-reducing capabilities from a haloalkaline environment

The extracellular electron transfer (EET)-capable electroactive microorganisms (EAMs) play crucial roles in mineral cycling and interspecies electron transfer in different environments and are used as biocatalysts in microbial electrochemical technologies. Studying EAMs from extreme environments is desired to advance the electromicrobiology discipline, understanding their unique metabolic traits with implications to extreme microbiology, and develop specific bioelectrochemical applications. Here, we present a novel haloalkaliphilic bacterium named Geoalkalibacter halelectricus SAP-1, isolated from a microbial electroactive biofilm enriched from the haloalkaline lake sediments. It is a rod-shaped Gram-negative heterotrophic anaerobe that uses various carbon and energy sources and respires on soluble and insoluble terminal electron acceptors. Besides 16S-rRNA and whole-genome-based phylogeny, the GGDC values of 21.7 %, ANI of 78.5, and 2.77 % genomic DNA GC content difference with the closest validly named species Geoalkalibacter ferrihydriticus (DSM 17813^T ) confirmed its novelty. When grown with the solid-state electrode as the only electron acceptor, it produced 460±23 μA/cm² bioelectrocatalytic current, thereby confirming its electroactivity. Further electrochemical analysis revealed the presence of membrane redox components with high formal potentials, putatively involved in the direct mode of EET. These are distinct from EET components reported for any known electroactive microorganisms, including well-studied Geobacter spp., Shewanella spp. and Desulfuromonas acetexigens. Further the capabilities of G. halelectricus SAP-1 to respire soluble as well insoluble electron acceptors including fumarate, SO₄ ^2- , Fe³⁺ , and Mn⁴⁺ suggests its role in cycling these elements in haloalkaline environments. This article is protected by copyright. All rights reserved.

Oligotrophy vs. copiotrophy in an alkaline and saline habitat of Lonar Lake

We reported our comparative observations on oligotrophs vs. copiotrophs from a hyper-alkaline and hypersaline habitat, Lonar Lake, situated in the Buldhana district of Maharashtra, India. Cell numbers of oligotrophic and copiotrophic microbes from the sediment were enumerated by the three-tube most probable number (MPN) method using an array of nutrient-rich and oligotrophic (≈10–20 mg carbon L−1) media offering simulated natural conditions of pH and salinity. A total of 50 strains from 15 different genera and 30 different species were isolated from the highest positive dilutions of MPN to identify the taxa of oligotrophs and copiotrophic microorganisms dominating in Lonar Lake. We did not get any true oligotrophs due to their adaptation to higher carbon levels during the isolation procedure. On the contrary, several true copiotrophs, which could not adapt and survive on a low-carbon medium, were isolated. It is also observed that changes in medium composition and nutrient level altered the selection of organisms from the same sample. Our data indicate that copiotrophic microorganisms dominate the eutrophic Lonar Lake, which is also supported by the past metagenomics studies from the same site. We also reported that quick depletion of carbon from oligotrophic medium worked as a limiting factor, inducing cell death after 2–3 generations and preventing the development of visible colonies on plates and sufficient optical density in liquid medium. Therefore, a long-term supply of low levels of carbon, followed by isolation on enriched media, can serve as a good strategy in isolation of novel taxa of microorganism, with industrial or environmental importance.

Diversity of prokaryotic microorganisms in alkaline saline soil of the Qarhan Salt Lake area in the Qinghai-Tibet Plateau

The composition of microbial communities varies considerably across ecological environments, particularly in extreme environments, where unique microorganisms are typically used as the indicators of environmental conditions. However, the ecological reasons for the differences in microbial communities remain largely unknown. Herein, we analyzed taxonomic and functional community profiles via high-throughput sequencing to determine the alkaline saline soil bacterial and archaeal communities in the Qarhan Salt Lake area in the Qinghai–Tibet Plateau. The results showed that Betaproteobacteria (Proteobacteria) and Halobacteria (Euryarchaeota) were the most abundant in the soils of this area, which are common in high salinity environments. Accordingly, microbes that can adapt to local extremes typically have unique metabolic pathways and functions, such as chemoheterotrophy, aerobic chemoheterotrophy, nitrogen fixation, ureolysis, nitrate reduction, fermentation, dark hydrogen oxidation, and methanogenesis. Methanogenesis pathways include hydrogenotrophic methanogenesis, CO₂ reduction with H₂, and formate methanogenesis. Thus, prokaryotic microorganisms in high salinity environments are indispensable in nitrogen and carbon cycling via particular metabolic pathways.

Lonar Impact Crater, India: the Best-Preserved Terrestrial Hypervelocity Impact Crater in a Basaltic Terrain as a Potential Global Geopark

Lonar Impact Crater is a simple meteorite impact crater carved out on the ~ 65 Ma old Deccan tholeiitic flood basalts. The crater, though scoured in a basaltic terrain, is still preserved in its most pristine form, with a central crater lake. The geomorphology, geochemistry, geochronology, hydrology, geophysical parameters, and structural aspects of Lonar Crater have been explored in detail, but still continue to contribute valid scientific insights into the geology of terrestrial impact craters. Lonar serves as a potential analog site for studying impact cratering on planetary surfaces with basaltic terrains such as the Moon and Mars. Besides being a highly recognizable impact crater in India, the Lonar crater and its hinterland stand out with its archeological relevance and spiritual influence among the people. The numerous temples in and around the crater premises uphold the cultural significance of the region. The crater and adjacent areas are rich in flora and fauna representing a diverse ecosystem in the vastness of the arid Deccan Flood Basalts. Hence, the astrobleme and its surrounding is declared a Ramsar site and is also a protected wildlife sanctuary. The Indian Government has also declared the crater a National Geological Monument as well as an archaeological monument. Furthermore, the astrobleme is a unique site with socio-cultural and economic significance. With these plethoras of importance, combined with the geological and socio-cultural aspects in its hinterland, together with the most acclaimed UNESCO world heritage centers Ajantha and Ellora caves in the neighborhood, it stands as the right candidate for a UNESCO Global Geopark. However, the crater and its ecosystem are not preserved well enough, and the uniqueness of the crater is diminishing. But after selection as a Ramsar site, the area shows increased vegetation growth. The SWOT analysis conducted in this study accounts for Lonar Crater and its adjoining areas as a potential global geopark. Thus, through this study, we try to propagate the vivid and myriad importance of the Lonar crater and the necessity of protecting this geological monument from both anthropogenic and natural processes and to appraise the necessity for nominating this area as a UNESCO Global Geopark.

Fecal Streptococcus Alteration Is Associated with Gastric Cancer Occurrence and Liver Metastasis

The gut microbiome plays an indispensable role in the occurrence and progression of various diseases. However, its ability to predict gastric cancer (GC) and liver metastasis (GCLM) has not been fully identified. Fecal samples were collected from 49 GC patients (cancer group [group C]) and 49 healthy people (normal group [group N]) between 4 July 2020 and 9 March 2021. Furthermore, 26 patients with metastatic GC were divided into a liver metastatic group (group L) (n = 13) and a non-liver-metastatic group (group M) (n = 13). DNA was extracted, and 16S rRNA gene sequencing was performed. SPSS was used for statistical analyses, and all bioinformatics analyses were based on QIIME2. P values of <0.05 were considered statistically significant. The microbial richness and diversity in group C were higher than those in group N, and there were significant differences in species compositions between the two groups. Streptococcus, enriched in groups C and L by linear discriminant analysis (LDA) effect size (LEfSe) and further identified by a random forest (RF) model, enhances its potential as a biomarker for GC and GCLM. Functional gene and metabolic pathway analyses showed that d-galacturonate degradation pathway II was of great importance in the occurrence and development of GC. Streptococcus has the potential ability to predict GC and GCLM, which is critical for the early diagnosis of GC and GCLM.

Prokaryotic diversity and composition within equatorial lakes Olbolosat and Oloiden in Kenya (Africa)

Total community 16S rDNA was used to determine the diversity and composition of bacteria and archaea within lakes Olbolosat and Oloiden in Kenya. The V3-V4 hypervariable region of the 16S rRNA gene was targeted since it's highly conserved and has a higher resolution for lower rank taxa. High throughput sequencing was performed on 15 samples obtained from the two lakes using the Illumina Miseq platform. Lakes Olbolosat and Oloiden shared 280 of 10,523 Amplicon Sequence Variants (ASVs) recovered while the four sample types (water, microbial mats, dry and wet sediments) shared 4 ASVs. The composition of ASVs in lake Olbolosat was highly dependent on Cu+, Fe2+, NH4 +, and Mn2+, while L. Oloiden was dependent on Mg2+, Na+, Ca2+, and K+. All the alpha diversity indices except Simpson were highest in the dry sediment sample (EC1 and 2) both from lake Oloiden. The abundant phyla included Proteobacteria (33.8%), Firmicutes (27.3%), Actinobacteriota (21.2%), Chloroflexi (6.8%), Cyanobacteria (3.8%), Acidobacteriota (2.8%), Planctomycetota (1.9%) and Bacteroidota (1.1%). Analysis of similarity (ANOSIM) revealed a significant difference in ASV composition between the two lakes (r = 0.191, p = 0.048), and between the sample types (r = 0.6667, p = 0.001). The interaction network for prokaryotic communities within the two lakes displayed Proteobacteria to be highly positively connected with other microbes. PERMANOVA results suggest that temperature controls the functioning of the two ecosystems.

Tumor-Associated Microbiota in Proximal and Distal Colorectal Cancer and Their Relationships With Clinical Outcomes

The proximal and distal subsites of colorectal cancer (CRC) have distinct differences in their embryonic origin, epidemiology, and prognosis. Therefore, they are not considered as the same disease. However, the possible difference in microbial characterization of the two subsites of CRC is still unclear. In this study, we explored tumor microbiota diversity and composition difference in patients with proximal (N = 187) and distal CRCs (N = 142). This was carried out on cancer tissues and adjacent tissues using bacterial 16S rRNA sequencing. The Kaplan–Meier method was used to analyze the correlation between differential flora and overall survival rate of the patients. It was found that there were significant differences in tumor microbial characteristics between the proximal and distal CRC tissues. The microbiota communities were distinctly richer in the proximal colon tumor tissues than in the distal CRC tissues. Microbial diversity and structure were relatively constant in the paracancerous normal tissues of the proximal and distal colorectum. Generally, microbial communities of CRC tumor tissues were composed of Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Alpha diversity in the proximal and distal CRC tumor tissues was closely related to specific microflora. The abundance of Fusobacteria was associated with age of patient, tumor diameter, and tumor microsatellite instability (MSI) status of the patients. Moreover, Fusobacteria enrichment was associated with poor prognosis especially in patients with proximal colon cancers, but not in patients with distal CRC. In conclusion, proximal and distal subsites of the CRC present distinct microbiota diversity and community structures. The differences indicate that there are different risk factors across anatomical subsites of CRC, which may provide a new strategy for precise prevention and treatment of CRC in the future.

Genes associated with antibiotic tolerance and synthesis of antimicrobial compounds in a mangrove with contrasting salinities

Salinity and wastewater pollution in mangrove ecosystems can affect microorganisms and the abundance of genes involved in response to these stressors. This research aimed to identify genes associated with resistance and biosynthesis of antimicrobial compounds in mangrove soils subjected to contrasting salinities and wastewater pollution. Samples of rhizospheric soil were taken from a mangrove at the mouth of the Ranchería River in La Guajira, Colombia. A functional analysis was performed using Illumina HiSeq 2500 sequencing data obtained from total DNA extracted. Increased salt concentration influenced metabolic pathways and differential abundance of genes associated with the synthesis of antimicrobial compounds (e.g., rfbB/rffG, INO1/ISYNA1, rfbA/rffH, sat/met3, asd). Also, among 33 genes involved in intrinsic antibiotic resistance, 16 were significantly influenced by salinity (e.g., cusR/copR/silR, vgb, tolC). We concluded that salt stress tolerance and adaptive mechanisms could favor the biosynthesis of antimicrobial compounds in mangroves contaminated by sewage.

Electrochemical enrichment of haloalkaliphilic nitrate-reducing microbial biofilm at the cathode of bioelectrochemical systems

Electrotrophic microorganisms have not been well studied in extreme environments. Here, we report on the nitrate-reducing cathodic microbial biofilm from a haloalkaline environment. The biofilm enriched via electrochemical approach under 9.5 pH and 20 g NaCl/L salinity conditions achieved −43.5±7.2μA/cm2 current density and 49.5±13.2%nitrate reduction efficiency via partial and complete denitrification. Voltammetric characterization of the biocathodes revealed a redox center with −0.294±0.003V (vs. Ag/AgCl) formal potential putatively involved in the electron uptake process. The lack of soluble redox mediators and hydrogen-driven nitrate reduction suggests direct-contact cathodic electron uptake by the nitrate-reducing microorganisms in the enriched biofilm. 16S-rRNA amplicon sequencing of the cathodic biofilm revealed the presence of unreported Pseudomonas, Natronococcus, and Pseudoalteromonas spp. at 31.45%,11.82%, and 9.69% relative sequence abundances, respectively. The enriched nitrate-reducing microorganisms also reduced nitrate efficiently using soluble electron donors found in the lake sediments, thereby suggesting their role in N-cycling in such environments.

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Enrichment of haloalkaliphilic nitrate-reducing microbial biofilm at the cathode

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Cathodic reduction current corresponded to the nitrate reduction process

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Pseudomonas, Natronococcus, and Pseudoalteromonas spp. enriched in the cathodic biofilm

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Enriched culture reduced nitrate efficiently with soluble electron donor sources

Microbial Characteristics of Locally Advanced Rectal Cancer Patients After Neoadjuvant Chemoradiation Therapy According to Pathologic Response

Background

Intestinal microbiota play a critical role in the development of colorectal cancer. However, little is known about the structure and characteristics of gut microbial in colorectal cancer, especially in locally advanced rectal cancer after neoadjuvant chemoradiation therapy.

Methods

Here, we performed this study to evaluate microbial characteristics between pathologic complete response (pCR) (n=12) and non-pathological complete response (Non-pCR) (n=45) tumor tissues from patients with locally advanced rectal cancer after neoadjuvant chemoradiation therapy. In this study, 16S rRNA gene sequencing was used to detect the microbial diversity including Alpha diversity and Beta diversity. Moreover, we used PICRUSt from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to predict the microbial metabolism functions.

Results

There was significant statistical difference in PFS between pCR and Non-pCR group (p < 0.05). However, there was no significant difference in OS between pCR and Non-pCR group. The microbial compositions in the both groups were Proteobacteria, Actinobacteria, Firmicutes and Thermi and Bacteroidetes at the phylum level. The five most predominant genera in both pCR and Non-pCR tissue groups were Sphingobium, Acinetobacter, Cupriavidus, Thermi and Sphingomonas at the genus level. The key taxa identified in the pCR and Non-pCR tissues were Thermi and Sphingomonadaceae respectively. In addition, a series of human disease-related genes were also significantly different between pCR and Non-pCR group.

Conclusion

In summary, we demonstrated the characteristic differences in microbial communities between pCR tissues and Non-pCR tumor tissues from locally advanced rectal cancer patients after neoadjuvant chemoradiation therapy. Our results present new alterations in the microbiome in locally advanced rectal cancer after neoadjuvant chemoradiation therapy, suggesting that it will provide a new perspective for the precise treatment of neoadjuvant rectal cancer by targeting specific microbial species in the future.

Influence of Pelvic Intensity-Modulated Radiation Therapy With Concurrent Cisplatin-Based Chemotherapy of Cervical Cancer on the Vaginal Microbiome

Pelvic intensity-modulated radiation therapy (IMRT) combined with concurrent chemotherapy is an effective treatment for cervical cancer; however, radiation resistance impairs its clinical benefit. The vaginal microbiome plays an important but poorly understood role in cancer radiochemotherapy. In this study, we investigated the effects of treatment on the overall composition and alteration of the vaginal microbiome in patients receiving pelvic IMRT with concurrent cisplatin-based chemotherapy. We collected samples from twenty patients with cervical cancer and six healthy controls and performed 16S rRNA sequencing. Vaginal microbial composition analysis revealed significant differences between the two groups, but no significant differences between radiation treatment time points. However, the relative abundances of Gammaproteobacteria, Gemmatimonadetes, Gemmatimonadales, Pseudomonadales, Gemmatimonadaceae, Rikenellaceae, Acinetobacter, Desulfovibrio, Prevotella 9, Rikenellaceae RC9 gut group, Turicibacter, and the metagenome increased with time. The results encourage further study into the effects of the vaginal microbiome on cervical cancer treatment strategies, especially radiochemotherapy. Better understanding of these effects could inform new therapeutic approaches to enhance the efficacy of radiochemotherapy.

Spatio-temporal resolution of taxonomic and functional microbiome of Lonar soda lake of India reveals metabolic potential for bioremediation

Lonar Lake, India; a hypersaline and hyperalkaline extremophilic ecosystem having a unique microbial population has been rarely explored for bioremediation aspects. MinION-based shotgun sequencing was used to comprehensively compare the microbial diversity and functional potential of xenobiotic degradation pathways with seasonal changes. Proteobacteria and Firmicutes were prevalent bacterial phyla in the pre-monsoon and post-monsoon samples. Functional analysis from SEED-subsystem and KEGG database revealed 28 subsystems and 18 metabolic pathways for the metabolism of aromatic compounds and xenobiotic biodegradation respectively. Occurrence of N-phenyl alkanoic, benzoate, biphenyl, chloroaromatic, naphthalene, and phenol degradation genes depicted varied abundance in the pre-monsoon and post-monsoon samples. Further, KEGG analysis indicated nitrotoluene degradation pathway (ko00633) abundant in post-monsoon samples, and the benzoate degradation pathway (ko00362) predominant in 19LN4S (pre-monsoon) than 18LN7S (post-monsoon) samples. The abundant genes for benzoate degradation were pcaI: 3-oxoadipate CoA-transferase, alpha subunit, pcaH: protocatechuate 3,4-dioxygenase, beta subunit, and pcaB: 3-carboxy-cis, cis-muconate cycloisomerase, and 4-oxalocrotonate tautomerase. This metagenomic study provides a unique blueprint of hitherto unexplored xenobiotic biodegradation genes/pathways in terms of seasonal variations in the Lonar Lake, and warrants active exploitation of microbes for bioremediation purposes.

Bacillus subtilis CtpxS2-1 induces systemic resistance against anthracnose in Andean lupin by lipopeptide production

OBJECTIVE

To evaluate the role of the biocontrol agent Bacillus subtilis CtpxS2-1 in inducing lupin systemic resistance against anthracnose caused by Colletotrichum acutatum by lipopeptide production.

RESULTS

First, growth inhibition and thin layer chromatography-bioautography analysis confirmed that CtpxS2-1 cultures and their lipopeptide extracts, specifically fengycin, have strong antifungal activity against C. acutatum. Subsequent microscopic examination of these fungal inhibition zones showed mycelial pathogen deformations. PCR amplification of CtpxS2-1 confirmed the presence of genes encoding fengycins E and C, bacillomycin C, iturin A, and surfactins B and C. Based on this evidence, the effect of CtpxS2-1 and its lipopeptides on the induction of the lupin defence- and growth-related genes PR-1, PR-4, SOD-2, PIN-1 and PIN-3 was evaluated by RT-qPCR. In seedlings from roots treated with CtxpS2-1, a significant increase in the expression of these genes was induced. Efficacy assays showed that CtpxS2-1 treatment completely controlled anthracnose incidence (0.0%) compared with the untreated control. Furthermore, root and shoot growth in treated seedlings with CtpxS2-1 significantly increased due to disease control, as did the synthesis of the defence enzymes catalase, peroxidase and superoxide dismutase.

CONCLUSION

B. subtilis CtpxS2-1 is a key factor enhancing Andean lupin health by producing lipopeptides that damage C. acutatum cellular structures and inhibit their growth, as well as by inducing the expression of defence-related genes of lupin plants involved in systemic acquired resistance (SAR) against anthracnose.

Microbial electroactive biofilms dominated by Geoalkalibacter spp. from a highly saline-alkaline environment

Understanding of the extreme microorganisms that possess extracellular electron transfer (EET) capabilities is pivotal to advance electromicrobiology discipline and to develop niche-specific microbial electrochemistry-driven biotechnologies. Here, we report on the microbial electroactive biofilms (EABs) possessing the outward EET capabilities from a haloalkaline environment of the Lonar lake. We used the electrochemical cultivation approach to enrich haloalkaliphilic EABs under 9.5 pH and 20 g/L salinity conditions. The electrodes controlled at 0.2 V vs. Ag/AgCl yielded the best-performing biofilms in terms of maximum bioelectrocatalytic current densities of 548 ± 23 and 437 ± 17 µA/cm² with acetate and lactate substrates, respectively. Electrochemical characterization of biofilms revealed the presence of two putative redox-active moieties with the mean formal potentials of 0.183 and 0.333 V vs. Ag/AgCl, which represent the highest values reported to date for the EABs. 16S-rRNA amplicon sequencing of EABs revealed the dominance of unknown Geoalkalibacter sp. at ~80% abundance. Further investigations on the haloalkaliphilic EABs possessing EET components with high formal potentials might offer interesting research prospects in electromicrobiology.

Hydrological and soil physiochemical variables determine the rhizospheric microbiota in subtropical lakeshore areas

Background

Due to intensive sluice construction and other human disturbances, lakeshore vegetation has been destroyed and ecosystems greatly changed. Rhizospheric microbiota constitute a key part of a functioning rhizosphere ecosystem. Maintaining rhizosphere microbial diversity is a central, critical issue for sustaining these rhizospheric microbiota functions and associated ecosystem services. However, the community composition and abiotic factors influencing rhizospheric microbiota in lakeshore remain largely understudied.

Methods

The spatiotemporal composition of lakeshore rhizospheric microbiota and the factors shaping them were seasonally investigated in three subtropical floodplain lakes (Lake Chaohu, Lake Wuchang, and Lake Dahuchi) along the Yangtze River in China through 16S rRNA amplicon high-throughput sequencing.

Results

Our results showed that four archaeal and 21 bacterial phyla (97.04 ± 0.25% of total sequences) dominated the rhizospheric microbiota communities of three lakeshore areas. Moreover, we uncovered significant differences among rhizospheric microbiota among the lakes, seasons, and average submerged depths. The Acidobacteria, Actinobacteria, Bacteroidetes, Bathyarchaeota, Gemmatimonadetes, and Proteobacteria differed significantly among the three lakes, with more than half of these dominant phyla showing significant changes in abundance between seasons, while the DHVEG-6, Ignavibacteriae, Nitrospirae, Spirochaetes, and Zixibacteria varied considerably across the average submerged depths (n = 58 sites in total). Canonical correspondence analyses revealed that the fluctuation range of water level and pH were the most important factors influencing the microbial communities and their dominant microbiota, followed by total nitrogen, moisture, and total phosphorus in soil. These results suggest a suite of hydrological and soil physiochemical variables together governed the differential structuring of rhizospheric microbiota composition among different lakes, seasons, and sampling sites. This work thus provides valuable ecological information to better manage rhizospheric microbiota and protect the vegetation of subtropical lakeshore areas.

Pan-genome analysis of Paenibacillus polymyxa strains reveals the mechanism of plant growth promotion and biocontrol

Rapid development of gene sequencing technologies has led to an exponential increase in microbial sequencing data. Genome research of a single organism does not capture the changes in the characteristics of genetic information within a species. Pan-genome analysis gives us a broader perspective to study the complete genetic information of a species. Paenibacillus polymyxa is a Gram-positive bacterium and an important plant growth-promoting rhizobacterium with the ability to produce multiple antibiotics, such as fusaricidin, lantibiotic, paenilan, and polymyxin. Our study explores the pan-genome of 14 representative P. polymyxa strains isolated from around the world. Heap's law model and curve fitting confirmed an open pan-genome of P. polymyxa. The phylogenetic and collinearity analyses reflected that the evolutionary classification of P. polymyxa strains are not associated with geographical area and ecological niches. Few genes related to phytohormone synthesis and phosphate solubilization were conserved; however, the nif cluster gene associated with nitrogen fixation exists only in some strains. This finding is indicative of nitrogen fixing ability is not stable in P. polymyxa. Analysis of antibiotic gene clusters in P. polymyxa revealed the presence of these genes in both core and accessory genomes. This observation indicates that the difference in living environment led to loss of ability to synthesize antibiotics in some strains. The current pan-genomic analysis of P. polymyxa will help us understand the mechanisms of biological control and plant growth promotion. It will also promote the use of P. polymyxa in agriculture.

Metagenomic Insights Into the Diversity of Halophilic Microorganisms Indigenous to the Karak Salt Mine, Pakistan

Hypersaline regions are terrestrial analogs of the Earth’s primitive ecosystem and extraterrestrial environment. The salt range in Pakistan is considered among a few of the ancient salt deposits in the subcontinent. Karak salt mine is situated at the Northwest end in Pakistan. Despite the fact that halophiles initiated the formation of terrestrial ecosystems, their products and identities remain hidden. Some preliminary studies limited to culture-dependent isolations have been reported. Characterizing the microbiome that spans over centuries of ecosystem development is crucial, given their role in shaping landscape succession and biogeochemical cycles. Here, we used metagenomics techniques to explore the microbial diversity of the Karak salt mine. We used 16S rRNA Illumina amplicon sequencing to characterize the halophilic communities entrapped in Karak mine. The results were interpreted using Illumina Basespace, QIIME, and Cytoscape. Cultures were isolated at 16–25% salinity. Metagenomics data was consistent with our preliminary culturing data, indicating remarkable species to strain-level diversity of unique halophiles. A total of 107,099 (brine) and 122,679 (salt) reads were obtained. 16S rRNA based sequencing revealed a microbiome with bacteria (66% brine and 72% salt) dominated by Bacteroidetes and Proteobacteria with a strikingly high abundance of Archaea (18% brine and 13% salt). Alpha diversity has higher values in salt than in the brine. The study of the halophiles in the Karak salt mine provides clues for species contributing to the maintenance of biogeochemical cycles of the ecosystem. This is the first report of a metagenomic study of any hypersaline region of Pakistan.

Distribution of Endocrine Disruptor Chemicals and Bacteria in Saline Pétrola Lake (Albacete, SE Spain) Protected Area is Strongly Linked to Land Use

Saline lakes are subject to numerous environmental impacts related to human activities, changing the chemical and biological natural conditions of the ecosystem. Sustainable development depends on the conservation of such delicate saline ecosystems, which may hold distinctive biodiversity. Pollution is one of the major threats to surface water bodies, for example by increasing nutrient contents and organic pollutants, including endocrine disrupting chemicals. Microbially mediated redox processes exert a fundamental control on nutrient turnover and contaminant removal. This study examines the influence of land use on the distribution of endocrine disrupting chemicals as well as on the microbial community composition in lacustrine sediments from Pétrola saline Lake (SE Spain). The lake is impacted by anthropogenic activities (agriculture, farming, mining and urban wastewater spills). Applying chemical and molecular tools (sequencing of 16S rRNA gene) showed a clear influence of land use on the chemistry and bacterial abundance of the lake sediments. The sampling points closer to wastewater outflows and mining ponds (2635, 2643 and 2650) showed fewer numbers and types of endocrine disrupting chemicals as well as a smaller number of families in the microbial community. These findings improve our understanding of how land use affects both water chemistry and the abundance of organisms responsible for biogeochemical cycles.

An evaluation of the core bacterial communities associated with hypersaline environments in the Qaidam Basin, China

Hypersaline lakes and saltern areas are important industrial and biodiversity resources in the Qaidam Basin of China that reside at > 2600 m asl. Most hypersaline environments in this area are characterized by saturated salinity (~ 300 g/L salinity), nearly neutral pH, intense ultraviolet radiation, and extremely variable temperature fluctuations. The core bacterial communities associated with these stressful environments have nevertheless remained uninvestigated. 16S rRNA gene Illumina sequencing analyses revealed that the bacterial communities were dominated by core lineages including the Proteobacteria (39.4-64.6%) and the Firmicutes (17.0-42.7%). However, the relative abundances of common lineages, and especially the five most abundant taxa of Pseudomonas, Lactococcus, Anoxybacillus, Acinetobacter, and Brevundimonas, were highly variable across communities and closely associated with hypersaline characteristics in the samples. Network analysis revealed the presence of co-occurrence high relative abundance taxa (cluster I) that were highly correlated across all hypersaline samples. Additionally, temperature, total organic carbon, K⁺, and Mg²⁺ correlated highest with taxonomic distributions across communities. These results highlight the potential mechanisms that could underlie survival and adaptation to these extreme hypersaline ecosystems.

Characterisation of hyper tolerant Bacillus firmus L-148 for arsenic oxidation

Groundwater arsenic pollution causes millions of deaths worldwide. Long term natural and anthropogenic activities have increased arsenic levels in groundwater causing higher threats of arsenic exposure. Arsenic hyper-tolerant Firmicute Bacillus firmus L-148 was isolated from arsenic limiting Lonar lake soil, which tolerated more than 3 M arsenic and could oxidize 75 mM arsenite [As(III)] in 14 days. It oxidized As(III) in presence of heavy metals and had unusual pH optima at 9.2. B. firmus L-148 was studied at the biochemical, protein, genomic and transcript level for understanding its arsenic oxidizing machinery. The proteomic and transcript analysis exhibited the presence of ars and aio operon and supported the inducible nature of ars operon. Robust, hyper-tolerant, fast As(III) oxidizing, least nutrient requiring and multi-metal resistance qualities of the strain were used in microcosm studies for bioremediation. Artificial groundwater mimicking microcosm with 75 mM As(III) was developed. Modulation of carbon source, iron and multi metals affected growth and As(III) oxidation rate. The As(III) oxidation was recorded to be 77% in 15 days in presence of sodium acetate and Fe ions. This microcosm study can be explored for bioremediation of arsenic contaminated water and followed by precipitation using other methods.

Shotgun metagenome guided exploration of anthropogenically driven resistomic hotspots within Lonar soda lake of India

Anthropogenic activities mediated antibiotic resistance genes (ARGs) in the pristine aquatic bodies (lakes) is raising concern worldwide. Long read shotgun sequencing was used to assess taxonomic diversity, distribution of ARGs and metal resistance genes (MRGs) and mobile genetic elements (MGEs) in six sites within hypersaline Lonar soda lake (India) prone to various anthropogenic activities. Proteobacteria and Euryarchaeota were dominant phyla under domain Bacteria and Archaea respectively. Higher abundance of Bacteroidetes was pragmatic at sites 18LN5 and 18LN6. Functional analysis indicated 26 broad-spectrum ARGs types, not reported earlier in this ecosystem. Abundant ARG types identified were multidrug efflux, glycopepetide, bacitracin, tetracycline and aminogylcoside resistance. Sites 18LN1 and 18LN5 depicted 167 and 160 different ARGs subtypes respectively and rpoB2, bcrA, tetA(48), mupA, ompR, patA, vanR and multidrug ABC transporter genes were present in all samples. The rpoB2 gene was dominant in 18LN1, whereas bcrA gene in 18LN2-18LN6 sites. Around 24 MRGs types were detected with higher abundance of arsenic in 18LN1 and copper in 18LN2-18LN6, signifying metal contamination linked to MRGs. The bacterial taxa Pseudomonas, Thioalkalivibrio, Burkholderia, Clostridium, Paenibacillus, Bacillus and Streptomyces were significantly associated with ARGs. This study highlights the resistomic hotspots in the lake for deploying policies for conservation efforts.

Analysis of by high-throughput sequencing: Helicobacter pylori infection and salivary microbiome

Background

There have been reports of Helicobacter pylori (H. pylori) in the oral cavity and it has been suggested that the oral cavity may be a reservoir for H. pylori reflux from the stomach. High-throughput sequencing was used to assess the structure and composition of oral microbiota communities in individuals with or without confirmed H. pylori infection.

Methods

Saliva samples were obtained from 34 H. pylori infected and 24 H. pylori uninfected subjects. Bacterial genomic DNA was extracted and examined by sequencing by amplification of the 16S rDNA V3-V4 hypervariable regions followed by bioinformatics analysis. Saliva sampling was repeated from 22 of the 34 H. pylori infected subjects 2 months after H. pylori eradication.

Results

High-quality sequences (2,812,659) clustered into 95,812 operational taxonomic units (OTUs; 97% identity). H. pylori was detected in the oral cavity in infected (12/34), uninfected (11/24) and eradicated (15/22) subjects by technique of high-throughput sequencing, occupying 0.0139% of the total sequences. Alpha diversity of H. pylori infected subjects was similar to that of uninfected subjects (Shannon: 1417.58 vs. 1393.60, p > 0.05, ACE: 1491.22 vs. 1465.97, p > 0.05, Chao 1: 1417.58 vs. 1393.60, p > 0.05, t-test). Eradication treatment decreased salivary bacterial diversity (Shannon, p = 0.015, ACE, p = 0.003, Chao 1, p = 0.002, t-test). Beta diversity analysis based on unweighted UniFrac distances showed that the salivary microbial community structure differed between H. pylori infected and uninfected subjects (PERMANOVAR, pseudo-F: 1.49, p = 0.033), as well as before and after H. pylori eradication (PERMANOVAR, pseudo-F: 3.34, p = 0.001). Using LEfSe analysis, 16 differentially abundant genera were defined between infected and uninfected subjects, 12 of which had a further alteration after successful eradication.

Conclusions

Our study using high-throughput sequencing showed that H. pylori was present commonly in the oral cavity with no clear relation to H. pylori infection of the stomach. Both H. pylori infection and eradication therapy caused alterations in community and structure of the oral microbiota.

Trial registration

clinicaltrials.gov, NCT03730766. Registered 2 Nov 2018 - Retrospectively registered, https://clinicaltrials.gov/ct2/show/ NCT03730766.

Data on genome sequencing, assembly, annotation and genomic analysis of Rhodococcus rhodochrous strain SPC17 isolated from Lonar Lake

The bacterial isolates of genus Rhodococcus are best known for their significant biodegradation abilities. Here, we report the data related to draft genome sequencing of Rhodococcus rhodochrous strain SPC17 isolated from sediments of Lonar Lake. The de novo assembly of 1598096 Illumina's paired-end sequencing reads resulted in 51 contigs for an overall genome assembly size of 4.98Mb. A total of 4546 genes were predicted using the National Center for Biotechnology Information- Prokaryotic Genome Annotation Pipeline (NCBI-PGAP). RAST server-based annotation of the Rhodococcus strain SPC17 genome resulted in a total of 295 subsystems with 25% subsystem coverage. The data on the draft genome shotgun project are accessible at NCBI-GenBank under the accession number WUUR00000000. Our data resource will facilitate further molecular and genomic studies of diverse hydrocarbon catabolizing genes present in Rhodococcus rhodochrous strain SPC17.

Spatio-temporal insights into microbiology of the freshwater-to-hypersaline, oxic-hypoxic-euxinic waters of Ursu Lake

Ursu Lake is located in the Middle Miocene salt deposit of Central Romania. It is stratified, and the water column has three distinct water masses: an upper freshwater-to-moderately saline stratum (0-3 m), an intermediate stratum exhibiting a steep halocline (3-3.5 m), and a lower hypersaline stratum (4 m and below) that is euxinic (i.e. anoxic and sulphidic). Recent studies have characterized the lake's microbial taxonomy and given rise to intriguing ecological questions. Here, we explore whether the communities are dynamic or stable in relation to taxonomic composition, geochemistry, biophysics, and ecophysiological functions during the annual cycle. We found: (i) seasonally fluctuating, light-dependent communities in the upper layer (≥0.987-0.990 water-activity), a stable but phylogenetically diverse population of heterotrophs in the hypersaline stratum (water activities down to 0.762) and a persistent plate of green sulphur bacteria that connects these two (0.958-0.956 water activity) at 3-3.5 to 4 m; (ii) communities that might be involved in carbon- and sulphur-cycling between and within the lake's three main water masses; (iii) uncultured lineages including Acetothermia (OP1), Cloacimonetes (WWE1), Marinimicrobia (SAR406), Omnitrophicaeota (OP3), Parcubacteria (OD1) and other Candidate Phyla Radiation bacteria, and SR1 in the hypersaline stratum (likely involved in the anaerobic steps of carbon- and sulphur-cycling); and (iv) that species richness and habitat stability are associated with high redox-potentials. Ursu Lake has a unique and complex ecology, at the same time exhibiting dynamic fluctuations and stability, and can be used as a modern analogue for ancient euxinic water bodies and comparator system for other stratified hypersaline systems.

Intestinal microbiome profiles in Oncomelania hupensis in mainland China

Oncomelania hupensis plays a significant role in the transmission of schistosomiasis japonica, which remains a major public health concern in China. Understanding the biological characteristics of O. hupensis is a prerequisite for its control; however, there are currently no studies investigating the intestinal microbiota of the O. hupensis snail. This study aimed to profile the intestinal microbiome of O. hupensis across different ecological landscapes in mainland China. DNA was extracted from the intestines of the collected snails and the bacterial communities were detected using 454 pyrosequencing. A total of 3,799 operational taxonomic units (OTUs) were obtained, and Proteobacteria, Firmicutes, and Actinobacteria were identified as the dominant bacterial taxa at the phylum level. Bacillus and Lactococcus were the most common genera in samples obtained from the four ecological landscapes. Snail specimens were clustered into three clades according to microbial community diversity, and thirty-seven genera that contributed to differential microbiota distributions were identified. Co-occurrence network analysis indicated a symbiotic relationship for the intestinal microbiota of O. hupensis, and PICRUSt analysis predicted forty-one metabolic functions in all snail samples, including membrane transport, amino acid metabolism, carbohydrate metabolism, replication and repair, energy metabolism, as well as xenobiotics biodegradation and metabolism. These findings improve our understanding of bacterial ecology in the O. hupensis intestine; further studies will focus on the relationship between O. hupensis intestinal microbiota and the microbiota in their specific ecological environments.

Microbiome and imputed metagenome study of crude and refined petroleum-oil-contaminated soils: Potential for hydrocarbon degradation and plant-growth promotion

Microbial community structure of crude petroleum oil (CP)- and refined petroleum oil (RP)-contaminated soil was investigated. The taxonomical and functional diversity of such soils can be a great source of information about microbial community and genes involved in petroleum hydrocarbon (PHC) degradation. In this study, microbial diversity of soils contaminated by RP from urban biome of Pune, India, and CP from agricultural biome of Gujarat, India, were assessed by 16S rRNA amplicon sequencing on Illumina MiSeq platform. Association between the soil microbial community and the physicochemical parameters were investigated for their potential role. In RP- and CP-contaminated soils, the microbiome analysis showed Proteobacteria as most dominant phylum followed by Actinobacteria. Interestingly, Firmicutes were most prevailing in a CP-contaminated sample while they were least prevailing in RP-contaminated soils. Soil moisture content, total organic carbon and organic nitrogen content influenced the taxa diversity in these soils. Species richness was more in RP as compared to CP soils. Further prediction of metagenome using PICRUSt revealed that the RP and CP soils contain microbial communities with excellent metabolic potential for PHC degradation. Microbial community contributing to genes essential for soil health improvement and plant growth promotion was also gauged. Our analysis showed promising results for future bioaugmentation assisted phytoremediation (BAP) strategies for treating such soils.

Effects of protease and phytase supplements on small intestinal microbiota and amino acid digestibility in broiler chickens

The objective of this study was to determine the effects of protease origin and dosage on the prececal (pc) amino acid (AA) digestibility and the influence on composition of the microbial community in the small intestine. In addition, the effects of phytase supplementation were investigated. A total of 8 dietary treatments were included. The basal diet contained mainly corn and soybean meal. Three protease products were added to the basal diet, each at the level recommended by the supplier and at an 8-fold level. Phytase was supplemented in another dietary treatment. Each dietary treatment was allocated to 8 replicates of 15 birds each. The experimental diets were offered from day 15 to 21 for ad libitum consumption. The effect of protease supplementation on the pc AA digestibility depended on the protease product type and the amount supplemented. The pc AA digestibility was significantly increased by 1 protease product when supplemented at high level and when phytase was supplemented. In all the other treatments, protease supplementation had no significant influence or it decreased pc AA digestibility, when compared with the treatment with no enzymes added. In general, Firmicutes was the most abundant phylum among the ileal microbiota across all the treatments. Significant effects on microbiota composition were observed at the genus level for some but not all protease treatments and phytase supplementation. The genera Streptococcus, Lactobacillus, and uncultured Clostridiaceae were responsible for these differences. Furthermore, microbial networks established for each diet showed either high or low number of intergeneric interactions, but without a consistent enzyme effect. We conclude that enzyme supplementation effects were evident in the terminal small intestine microbiota composition, and to a lesser extent, in pc AA digestibility. However, the changes in microbiota composition and pc AA digestibility could not be correlated, indicating absence of a causal relationship.

Survival of Extremotolerant Bacteria from the Mukundpura Meteorite Impact Crater

Carbonaceous meteorites provide clues with regard to prebiotic chemistry and the origin of life. Geological Survey of India recorded a carbonaceous chondrite meteorite fall in Mukundpura, India, on June 6, 2017. We conducted a study to investigate the microbial community that survived the meteorite impact. 16S rRNA metagenomic sequencing indicates the presence of Actinobacteria, Proteobacteria, and Acidobacteria in meteorite impact soil. Comparative phylogenetic analysis revealed an intriguing abundance of class Bacilli in the impact soil. Bacillus thermocopriae IR-1, a moderately thermotolerant organism, was isolated from a rock, impacted by the Mukundpura meteorite. We investigated the resilience of B. thermocopriae IR-1 to environmental stresses and impact shock in a Reddy shock tube. Bacillus thermocopriae IR-1 survived (28.82% survival) the effect of shock waves at a peak shock pressure of 300 kPa, temperature 400 K, and Mach number of 1.47. This investigation presents the first report on the effect of impact shock on B. thermocopriae IR-1. The study is also the first report on studying the microbial diversity and isolation of bacteria from impact crater soil immediately after meteorite impact event.

A glimpse of the prokaryotic diversity of the Large Aral Sea reveals novel extremophilic bacterial and archaeal groups

During the last five decades, the Aral Sea has gradually changed from a saline water body to a hypersaline lake. Microbial community inhabiting the Aral Sea has been through a succession and continuous adaptation during the last 50 years of increasing salinization, but so far, the microbial diversity has not been explored. Prokaryotic diversity of the Large Aral Sea using cultivation‐independent methods based on determination of environmental 16S rRNA gene sequences revealed a microbial community related to typical marine or (hyper) saline‐adapted Bacteria and Archaea. The archaeal sequences were phylogenetically affiliated with the order Halobacteriales, with a large number of operational taxonomic units constituting a novel cluster in the Haloferacaceae family. Bacterial community analysis indicated a higher diversity with representatives belonging to Proteobacteria, Actinobacteria and Bacteroidetes. Many members of Alphaproteobacteria and Gammaproteobacteria were affiliated with genera like Roseovarius, Idiomarina and Spiribacter which have previously been found in marine or hypersaline waters. The majority of the phylotypes was most closely related to uncultivated organisms and shared less than 97% identity with their closest match in GenBank, indicating a unique community structure in the Large Aral Sea with mostly novel species or genera.

Salino-alkaline lime of anthropogenic origin a reservoir of diverse microbial communities

This paper presents study on the microbiome of a unique extreme environment - saline and alkaline lime, a by-product of soda ash and table salt production in Janikowo, central Poland. High-throughput 16S rDNA amplicon sequencing was used to reveal the structure of bacterial and archaeal communities in the lime samples, taken from repository ponds differing in salinity (2.3-25.5% NaCl). Surprisingly abundant and diverse bacterial communities were discovered in this extreme environment. The most important geochemical drivers of the observed microbial diversity were salinity, calcium ions, nutrients, and water content. The bacterial and archaeal communities in saline, alkaline lime were similar to those found in natural haloalkaline environments. Although the archaeal contribution to the whole microbial community was lower than 4%, the four archaeal genera Natronomonas, Halorubrum, Halobellus, and Halapricum constituted the core microbiome of saline, alkaline lime - a set of OTUs (> 0.1% of total archaeal relative abundance) present in all samples under study. The high proportion of novel, unclassified archaeal and bacterial sequences (not identified at 97% similarity level) in the 16S rRNA gene libraries indicated that potentially new genera, especially within the class of Thermoplasmata inhabit this unique environment.

Shift in Bacterial Community Structure Drives Different Atrazine-Degrading Efficiencies

Compositions of pollutant-catabolic consortia and interactions between community members greatly affect the efficiency of pollutant catabolism. However, the relationships between community structure and efficiency of catabolic function in pollutant-catabolic consortia remain largely unknown. In this study, an original enrichment (AT) capable of degrading atrazine was obtained. And two enrichments - with a better/worse atrazine-degrading efficiency (ATB/ATW) - were derived from the original enrichment AT by continuous sub-enrichment with or without atrazine. Subsequently, an Arthrobacter sp. strain, AT5, that was capable of degrading atrazine was isolated from enrichment AT. The bacterial community structures of these three enrichments were investigated using high-throughput sequencing analysis of the 16S rRNA gene. The atrazine-degrading efficiency improved as the abundance of Arthrobacter species increased in enrichment ATB. The relative abundance of Arthrobacter was positively correlated with those of Hyphomicrobium and Methylophilus, which enhanced atrazine degradation via promoting the growth of Arthrobacter. Furthermore, six genera/families such as Azospirillum and Halomonas showed a significantly negative correlation with atrazine-degrading efficiency, as they suppressed atrazine degradation directly. These results suggested that atrazine-degrading efficiency was affected by not only the degrader but also some non-degraders in the community. The promotion and suppression of atrazine degradation by Methylophilus and Azospirillum/Halomonas, respectively, were experimentally validated in vitro, showing that shifts in both the composition and abundance in consortia can drive the change in the efficiency of catabolic function. This study provides valuable information for designing enhanced bioremediation strategies.

Genome size evolution in the Archaea

What determines variation in genome size, gene content and genetic diversity at the broadest scales across the tree of life? Much of the existing work contrasts eukaryotes with prokaryotes, the latter represented mainly by Bacteria. But any general theory of genome evolution must also account for the Archaea, a diverse and ecologically important group of prokaryotes that represent one of the primary domains of cellular life. Here, we survey the extant diversity of Bacteria and Archaea, and ask whether the general principles of genome evolution deduced from the study of Bacteria and eukaryotes also apply to the archaeal domain. Although Bacteria and Archaea share a common prokaryotic genome architecture, the extant diversity of Bacteria appears to be much higher than that of Archaea. Compared with Archaea, Bacteria also show much greater genome-level specialisation to specific ecological niches, including parasitism and endosymbiosis. The reasons for these differences in long-term diversification rates are unclear, but might be related to fundamental differences in informational processing machineries and cell biological features that may favour archaeal diversification in harsher or more energy-limited environments. Finally, phylogenomic analyses suggest that the first Archaea were anaerobic autotrophs that evolved on the early Earth.

Characterization of the bacterial communities on recent Icelandic volcanic deposits of different ages

Background

Basalt is the most common igneous rock on the Earth’s surface covering. Basalt-associated microorganisms drive the cycling and sequestration of different elements such as nitrogen, carbon and other nutrients, which facilitate subsequent pioneer and plant development, impacting long-term regulation of the Earth’s temperature and biosphere. The initial processes of colonization and subsequent rock weathering by microbial communities are still poorly understood and relatively few data are available on the diversity and richness of the communities inhabiting successive and chronological lava flows. In this study, the bacterial communities present on lava deposits from different eruptions of the 1975–84 Krafla Fires (32-, 35- and 39-year old, respectively) at the Krafla, Iceland, were determined.

Results

Three sites were sampled for each deposit (32-, 35- and 39-year old), two proximal sites (at 10 m distance) and one more distant site (at 100 m from the two other sites). The determined chemical composition and metal concentrations were similar for the three basalt deposits. No significant differences were observed in the total number of cells in each flow. 16S rRNA gene amplicon sequencing showed that the most abundant classified phylum across the 3 flows was Proteobacteria, although predominance of Acidobacteria, Actinobacteria and Firmicutes was observed for some sampling sites. In addition, a considerable fraction of the operational taxonomic units remained unclassified. Alpha diversity (Shannon, inverse Simpson and Chao), HOMOVA and AMOVA only showed a significant difference for Shannon between the 32- and 39-year old flow (p < 0.05). Nonmetric multidimensional scaling (NMDS) analysis showed that age significantly (p = 0.026) influenced the leftward movement along NMDS axis 1.

Conclusions

Although NMDS indicated that the (relatively small) age difference of the deposits appeared to impact the bacterial community, this analysis was not consistent with AMOVA and HOMOVA, indicating no significant difference in community structure. The combined results drive us to conclude that the (relatively small) age differences of the deposits do not appear to be the main factor shaping the microbial communities. Probably other factors such as spatial heterogeneity, associated carbon content, exogenous rain precipitations and wind also affect the diversity and dynamics.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1262-0) contains supplementary material, which is available to authorized users.

Desiccation- and Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments

More than 41% of the Earth's land area is covered by permanent or seasonally arid dryland ecosystems. Global development and human activity have led to an increase in aridity, resulting in ecosystem degradation and desertification around the world. The objective of the present work was to investigate and compare the microbial community structure and geochemical characteristics of two geographically distinct saline pan sediments in the Kalahari Desert of southern Africa. Our data suggest that these microbial communities have been shaped by geochemical drivers, including water content, salinity, and the supply of organic matter. Using Illumina 16S rRNA gene sequencing, this study provides new insights into the diversity of bacteria and archaea in semi-arid, saline, and low-carbon environments. Many of the observed taxa are halophilic and adapted to water-limiting conditions. The analysis reveals a high relative abundance of halophilic archaea (primarily Halobacteria), and the bacterial diversity is marked by an abundance of Gemmatimonadetes and spore-forming Firmicutes. In the deeper, anoxic layers, candidate division MSBL1, and acetogenic bacteria (Acetothermia) are abundant. Together, the taxonomic information and geochemical data suggest that acetogenesis could be a prevalent form of metabolism in the deep layers of a saline pan.

Pediatric Obstructive Sleep Apnea is Associated With Changes in the Oral Microbiome and Urinary Metabolomics Profile: A Pilot Study

STUDY OBJECTIVES

Several cross-sectional studies have reported associations between oral diseases and obstructive sleep apnea (OSA). However, there have been no reports regarding the structure and composition of the oral microbiota with simultaneous evaluation of potential associations with perturbed metabolic profiles in pediatric OSA.

METHODS

An integrated approach, combining metagenomics based on high-throughput 16S rRNA gene sequencing, and metabolomics based on ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry and gas chromatography coupled with time-of-flight mass spectrometry, was used to evaluate the oral microbiome and the urinary metabolome.

RESULTS

16S rRNA gene sequencing indicated that the oral microbiome composition was significantly perturbed in pediatric OSA compared with normal controls, especially with regard to Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, and Actinobacteria. Moreover, metabolomics profiling indicated that 57 metabolites, 5 of which were metabolites related to the microflora of the digestive tract, were differentially present in the urine of pediatric patients with OSA and controls. Co-inertia and correlation analyses revealed that several oral microbiome changes were correlated with urinary metabolite perturbations in pediatric OSA. However, this correlation relationship does not imply causality.

CONCLUSIONS

High-throughput sequencing revealed that the oral microbiome composition and function were significantly altered in pediatric OSA. Further studies are needed to confirm and determine the mechanisms underlying these findings.

Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method

Intertidal mudflats are land–sea interaction areas and play important roles in global nutrient cycles. However, a comprehensive understanding of microbial communities in these mudflats remains elusive. In this study, mudflat sediment samples from the Dongtan wetland of Chongming Island, the largest alluvial island in the world, were collected. Using a modified metatranscriptomic method, the depth-wise distributions of potentially active microbial communities were investigated based on small subunit ribosomal RNA (SSU rRNA) sequences. Multiple environmental factors were also measured and analyzed in conjunction with the prokaryotic composition profiles. A prokaryotic diversity analysis based on the metatranscriptome datasets revealed two or threefold higher diversity indices (associated with potentially active microbes participating in biogeochemical processes in Dongtan) compared with the diversity indices based on 16S rRNA gene amplicons. Bacteria were numerically dominant relative to archaea, and the potentially active prokaryotic taxa were mostly assigned to the bacterial phyla Chloroflexi, Acidobacteria, and Bacteroidetes and the classes Delta- and Gamma-proteobacteria, along with the archaeal lineages phylum Bathyarchaeota and the order Thermoplasmatales. The total nitrogen and carbon content of the sediment samples were environmental factors that significantly affected the depth-wise distributions of both bacterial and archaeal communities. Furthermore, the activity of potentially active taxa (including the prevalent order Desulfobacterales and family Anaerolineaceae) appeared to be significantly underestimated by PCR-based methods, notably at the DNA level, and indicates that using normal PCR amplification of DNA limits the study of potential microbial activity. This is the first study of potentially active microbial communities in depth-wise sediments from Dongtan. The improved knowledge of microbial communities in Dongtan provides a foundation for exploring biogeochemical cycling and microbial functions.