Bacterial Diversity in an Alpine Debris-Free and Debris-Cover Accumulation Zone Glacier Ice, North Sikkim, India

Habitat-specific patterns of bacterial communities in a glacier-fed lake on the Tibetan Plateau

Different types of inlet water are expected to affect microbial communities of lake ecosystems due to changing environmental conditions and the dispersal of species. However, knowledge of the effects of changes in environmental conditions and export of microbial assemblages on lake ecosystems is limited, especially for glacier-fed lakes. Here, we collected water samples from the surface water of a glacier-fed lake and its two fed streams on the Tibetan Plateau to investigate the importance of glacial and non-glacial streams as sources of diversity for lake bacterial communities. Results showed that the glacial stream was an important source of microorganisms in the studied lake, contributing 45.53% to the total bacterial community in the lake water, while only 19.14% of bacterial community in the lake water was seeded by the non-glacial stream. Bacterial communities were significantly different between the glacier-fed lake and its two fed streams. pH, conductivity, total dissolved solids, water temperature and total nitrogen had a significant effect on bacterial spatial turnover, and together explained 36.2% of the variation of bacterial distribution among habitats. Moreover, bacterial co-occurrence associations tended to be stronger in the lake water than in stream habitats. Collectively, this study may provide an important reference for assessing the contributions of different inlet water sources to glacier-fed lakes.

Diversity and co-occurrence networks of bacterial and fungal communities on two typical debris-covered glaciers, southeastern Tibetan Plateau

Debris-covered glaciers (DCGs) are globally distributed and thought to contain greater microbial diversity than clean surface continental glaciers, but the ecological characteristics of microbial communities on the surface of DCGs have remained underexplored. Here, we investigated bacterial and fungal diversity and co-occurrence networks on the supraglacial debris habitat of two DCGs (Hailuogou and Dagongba Glaciers) in the southeastern Tibetan Plateau. We found that the supraglacial debris harbored abundant microbes with Proteobacteria occupying more than half (51.5%) of the total bacteria operational taxonomic units. The composition, diversity, and co-occurrence networks of both bacterial and fungal communities in the debris were significantly different between Hailuogou Glacier and Dagongba Glacier even though the glaciers are geographically adjacent within the same mountain range. Bacteria were more diverse in the debris of the Dagongba Glacier, where a lower surface velocity and thicker debris layer allowed the supraglacial debris to continuously weather and accumulate nutrients. Fungi were more diverse in the debris of the Hailuogou Glacier, which experiences a wetter monsoonal climate, is richer in calcium, has greater debris instability, and greater ice velocity than the Dagongba Glacier. These factors may provide ideal conditions for the dispersal and propagation of fungi spores on the Hailuogou Glacier. In addition, we found an obvious gradient of bacterial diversity along the supraglacial debris transect on the Hailuogou Glacier. Bacterial diversity was lower where debris cover was thin and scattered and became more diverse near the glacial terminus in thick, slow-moving debris. No such increasing bacterial pattern was detected on the Dagongba Glacier, which implies a positive relationship of debris age, thickness, and weathering on bacterial diversity. Additionally, a highly connected bacterial co-occurrence network with low modularity was found in the debris of the Hailuogou Glacier. In contrast, debris from the Dagongba Glacier exhibited less connected but more modularized co-occurrence networks of both bacterial and fungal communities. These findings indicate that less disturbed supraglacial debris conditions are crucial for microbes to form stable communities on DCGs.

Contamination analysis of Arctic ice samples as planetary field analogs and implications for future life-detection missions to Europa and Enceladus

Missions to detect extraterrestrial life are being designed to visit Europa and Enceladus in the next decades. The contact between the mission payload and the habitable subsurface of these satellites involves significant risk of forward contamination. The standardization of protocols to decontaminate ice cores from planetary field analogs of icy moons, and monitor the contamination in downstream analysis, has a direct application for developing clean approaches crucial to life detection missions in these satellites. Here we developed a comprehensive protocol that can be used to monitor and minimize the contamination of Arctic ice cores in processing and downstream analysis. We physically removed the exterior layers of ice cores to minimize bioburden from sampling. To monitor contamination, we constructed artificial controls and applied culture-dependent and culture-independent techniques such as 16S rRNA amplicon sequencing. We identified 13 bacterial contaminants, including a radioresistant species. This protocol decreases the contamination risk, provides quantitative and qualitative information about contamination agents, and allows validation of the results obtained. This study highlights the importance of decreasing and evaluating prokaryotic contamination in the processing of polar ice cores, including in their use as analogs of Europa and Enceladus.

Draft genome sequence of Stenotrophomonas maltophilia strain P13 gives insight into its protease production and assessment of sulfur and nitrogen metabolism

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In this study draft genome sequence of Stenotrophomonas maltophilia strain P13 which was isolated from Kanchengayao glacier, North Sikkim, India.

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The genome of P13 strain possesses 2689,565 total reads, with an average G + C content of 69.9%.

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The major enzymes present are beta-galactosidase, thiol peroxidase, thiolredoxin reductase, glutamate synthase, and glutamate-ammonia-ligase adenyltransferase.

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FAME, morphological and biochemical characterization, and scanning electron microscopy (SEM) of Stenotrophomonas maltophilia strain P13 are provided.

Stenotrophomonas maltophilia strain P13 was isolated from the Kanchengayao glacier's accumulation zone. A comprehensive study was done on this strain as it produced protease enzyme and thus having industrial potential. The whole genome sequence, FAME, morphological and biochemical characteristics of the S. maltophilia strain P13 is being presented. The genome of P13 strain possesses 2,689,565 total reads, with an average G + C content of 69.9%. The whole-genome assembly is having 548 contigs (with PEGs). The genome contains 2,985 coding sequences with 55 rRNA predicted genes. More than 88% of the total pre-processed reads from samples were mapped. The identified coding proteins were classified into 27 functional categories based on COG classification. The genome was found to possess genes for ammonium assimilation, galactosylceramide and sulfatide metabolism. The major enzymes present are beta-galactosidase, thiol peroxidase, thiolredoxin reductase, glutamate synthase, and glutamate-ammonia-ligase adenyltransferase. The genome information of Stenotrophomonas maltophilia P13 provides the basis for understanding the functional properties and abilities to act as a potential cold-active enzyme producer and nitrogen-fixing bacteria.

Isolation and characterization of plant growth promoting rhizobacteria isolated from organically grown high yielding pole type native pea (Pisum sativum L.) variety Dentami of Sikkim, India

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The present research showcases the significant findings pertaining to the assessment and report of the first ever study on the isolation and identification of plant growth promoting rhizobacterial diversity of organic farming pea variety (Dentami) of Sikkim. Proteobacteria dominated the rhizospheric soil whereas the bulk soil was governed by Actinobacteria. Bacillus cereus P8 (66.5 µg ml⁻¹) and Bacillus mycoides PP1 (45.1 µg ml⁻¹) were the highest IAA producer and also showed other plant growth promoting and biocontrol traits, such as phosphorous and potassium solubilization, nitrogen-fixing activity and siderophore production. As, Sikkim is the first state in India to practice organic agriculture farming, hence, such study on the soil microbiology is of immense significance. In these rhizospheric soil, it was dominated by the Proteobacteria and similar bacterial isolates, suggesting that these soil flora might be playing significant roles to enhancing the crop production and soil fertility.

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Culture-dependent technique was used to assess plant growth promoting rhizobacterial diversity of pole type pea variety (Dentami) of Sikkim.

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The dominant phylum was Proteobacteria (56%) from rhizosphere soil and Actinobacteria (58%) from bulk soil.

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PCA analysis showed that Firmicutes (bulk soil) were positively correlated to SOC, and available K, whereas, Proteobacteria (rhizosphere soil) exhibited a high correlation to pH, and available P.

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Bacillus cereus P8, Arthrobacter woluwensis DP2, Paenarthrobacter nitroguajacolicus UP1, and Bacillus mycoides PP1 showed plant growth promotion and bio-control traits.

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Bacillus cereus P8 (66.5 µg mL⁻¹) and Bacillus mycoides PP1 (45.1 µg mL⁻¹) was thehighest IAA producer.

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Pot experiment confirmed that these isolates can be potential plant growth promoter under the agro-climatic conditions of Sikkim, India.

Organic farming is an eco-friendly and sustainable farming practice that enhances soil fertility and helps in improving soil quality. But with the commencement of more sophisticated advances in agricultural techniques, organic farming has gradually become limited in the world. Culture-dependent plant growth-promoting bacterial isolates were isolated from the bulk and rhizospheric soil, of the native high yielding pole type organic pea (Pisum sativum L.) cultivar Dentami of Dentam, West Sikkim, India. Based on the 16S rRNA gene sequencing identification of these isolates, it was found that from the bulk soil, Actinobacteria (58%) was the dominant phyla followed by Firmicutes (28%), and Proteobacteria (14%). In the rhizospheric soil it was dominated by Proteobacteria (56%), followed by Firmicutes (33%), and Bacteriodetes (11%). A total of 40 bacterial isolates were initially screened for the plant growth-promoting (PGP) activity and out of them only four bacterial isolates i.e., Bacillus cereus P8, Arthrobacter woluwensis DP2, Paenarthrobacter nitroguajacolicus PP3, and Bacillus mycoides PP10 with accession numbers MN589697, MN559516, MN519462 and MN589696 respectively were found to possess higher PGP activity (i.e. phosphorous, potassium solubilization and nitrogen-fixing activity) as compared to the other bacteria present in the soil. Based on the indole-3-acetic acid (IAA) quantitative assay and siderophore production assay, it was found that Bacillus cereus (MN589697) produced the highest IAA (65.5 µg mL⁻¹) and siderophore (71%) when compared with the other isolates. The statistical correlation suggests that pH and available phosphorus were the strongest influencing factors for the distribution of Proteobacteria in the rhizospheric soil. The results indicate that these isolates can be potential plant growth promoter under the agro-climatic conditions of Sikkim, India. To the best of our knowledge the present study is the first report of its kind and showcases significant findings pertaining to the assessment of diversity, isolation and identification of plant growth-promoting rhizobacteria of organic pea grown in Sikkim.

Isolation, Characterization, and Evaluation of Native Rhizobacterial Consortia Developed From the Rhizosphere of Rice Grown in Organic State Sikkim, India, and Their Effect on Plant Growth

Eight rhizospheric bacteria were isolated from the organic paddy fields of Sikkim, India, and identified as Pseudomonas kribbensis KSB, Burkholderia cenocepacia SRD, Kosakonia oryzendophytica YMA7, Pseudomonas rhodesiae SRB, Bacillus sp. ARA, Paenibacillus polymyxa COW3, Bacillus aryabhattai PSB2, and Bacillus megaterium PSB1. They showed plant growth-promoting attributes in rice and have bio-control potential against phytopathogen Colletotrichum gloeosporioides of large cardamom (Amomum subulatum). Burkholderia cenocepacia SRD showed production of indole acetic acid and ammonia and solubilization of phosphate and potassium and also possessed nitrogen fixation potential. It showed antagonistic activity against two other plant pathogens of large cardamom, viz., Curvularia eragrostidis and Pestalotiopsis sp., under in vitro conditions. The liquid bacterial consortium was prepared using the bacterial strains SRB, PSB1, and COW3 (Consortia-1); PSB2, SRD, and COW3 (Consortia-2); and COW3, KSB, and YMA7 (Consortia-3) to increase the growth and yield of rice plants under organic farming conditions. Greenhouse and field studies showed that the Consortia-3 had the highest plant growth-promoting activity. Consortia-3 demonstrated better agronomic performance in terms of root length (9.5 cm),number of leaflets per plant (5.3), grains per panicle (110.6), test grain weight (27.4 g), dry root weight per plant (0.73 g), and total dry biomass per plant (8.26 g).

Bacterial Diversity and Communities Structural Dynamics in Soil and Meltwater Runoff at the Frontier of Baishui Glacier No.1, China

Comprehensive knowledge of bacterial ecology mainly in supraglacial habitats is pivotal particularly at the frontier of accelerated glacier retreat. In this study, bacterial diversity and community composition in glacial soil and meltwater runoff at the frontier of Baishui Glacier No.1 were evaluated using high throughput sequencing. Significant variations in the physiochemical parameters formed an ecological gradient between soil and meltwater runoff. Based on the richness and evenness indexes, the bacterial diversity was relatively higher in soil compared with meltwater runoff. Hierarchical clustering and bi-plot ordination revealed that the taxonomic composition of soil samples was highly similar and significantly influenced by the ecological parameters than the meltwater runoff. The overall relative abundance trend of bacterial phyla and genera were greatly varied in soil and water samples. The relative abundance of Proteobacteria was higher in water runoff samples (40.5-87%) compared with soil samples (32-52.7%). Proteobacteria, Firmicutes, and a little part of Cyanobacteria occupied a major portion of water runoff while the soil was dominated by Acidobacteria (6-16.2%), Actinobacteria (5-16%), Bacteroidetes (0.5-8.8%), and Cyanobacteria (0.1-8.3%) besides Proteobacteria and Firmicutes. Higher numbers of biomarkers were found in soil group compared with the water group. The study area is diverse in terms of richness, while community structures are not evenly distributed. This study provides a preliminary understanding of the bacterial diversity and shifts in community structure in soil and meltwater runoff at the frontier of the glacial. The findings revealed that the environmental factors are a significantly strong determinant of bacterial community structures in such a closely linked ecosystem.

Exploration of Microbial Diversity of Himalayan Glacier Moraine Soil Using 16S Amplicon Sequencing and Phospholipid Fatty Acid Analysis Approaches

Changme Khangpu glacier is located in the northern district of Sikkim which comes under UNESCO heritage site Kanchenjunga Biosphere Reserve which is considered as one of the important biological hotspot regions in the Eastern Himalayas. This is the first report on microbial diversity analysis of moraine soil from one of the unexplored glaciers of Sikkim using high throughput sequencing platform and phospholipid fatty acids analysis (PLFA). It was found that the 16S amplicon sequence comprised 362,902 raw sequences with a sequence length of 150 bp and (G + C) content 52%. A total of 156,821 pre-processed reads were clustered into 378 OTUs (operational taxonomic units) comprising 6 bacterial phyla. The top four dominant phyla based on the 16S amplicon sequences were Proteobacteria (56%), Firmicutes (16%), Actinobacteria (12%), and Bacteroidetes (8%), respectively. PLFA analysis confirmed the dominance of Gram positive bacteria (72%) followed by Gram negative bacteria (32%) and the major fatty acids which are present in the moraine soil sample were PUFA (61%), and 18:2ω6,9c (29%). This is the primary study and first of its kind done on moraine soil from glaciers of Sikkim. Based on 16S amplicon sequencing and PLFA analysis of moraine soil samples from glaciers of Sikkim suggest that this glaciers harbours rich microbial diversity and thus can have wide industrial and biotechnological potential. Thus, there is an escalating scope to further study these extreme biomes with respect to their microbial diversity and their functional capabilities.

Distribution of antibiotic and metal resistance genes in two glaciers of North Sikkim, India

Glacier studies as of late have ruffled many eyeballs, exploring this frigid ecology to understand the impact of climate change. Mapquesting the glaciers led to the discovery of concealed world of "psychrophiles" harboring in it. In the present study, the antibiotic resistance genes (ARGs) and heavy metal resistance genes (MRGs) were evaluated through both the culture-dependent and culture-independent methods. Samples were collected from two different glaciers, i.e., debris-covered glacier (Changme Khangpu) and debris-free glacier (Changme Khang). Functional metagenomics of both the glacier samples, provided evidence of presence of resistant genes against various antibiotic groups. Bacitracin resistant gene (bacA) was the predominant ARG in both the glaciers. MRGs in both the glacier samples were diversified as the genes detected were resistant against various heavy metals such as arsenic, tungsten, mercury, zinc, chromium, copper, cobalt, and iron. Unique MRGs identified from Changme Khangpu glacier were resistant to copper (cutA, cutE, cutC, cutF, cueR, copC, and copB) and chromium (yelf, ruvB, nfsA, chrR, and chrA) whereas, from Changme Khang glacier they showed resistance against cobalt (mgtA, dmef, corD, corC, corB, and cnrA), and iron (yefD, yefC, yefB, and yefA) heavy metals. ARGs aligned maximum identity with Gram-negative psychrotolerant bacteria. The cultured bacterial isolates showed tolerance to high concentrations of tested heavy metal solutions. Interestingly, some of the antibiotic resistant bacterial isolates also showed tolerance towards the higher concentrations of heavy metals. Thus, an introspection of the hypothesis of co-occurrence and/co-selection of ARGs and MRGs in such environments has been highlighted here.

Microbial Ecology from the Himalayan Cryosphere Perspective

Cold-adapted microorganisms represent a large fraction of biomass on Earth because of the dominance of low-temperature environments. Extreme cold environments are mainly dependent on microbial activities because this climate restricts higher plants and animals. Himalaya is one of the most important cold environments on Earth as it shares climatic similarities with the polar regions. It includes a wide range of ecosystems, from temperate to extreme cold, distributed along the higher altitudes. These regions are characterized as stressful environments because of the heavy exposure to harmful rays, scarcity of nutrition, and freezing conditions. The microorganisms that colonize these regions are recognized as cold-tolerant (psychrotolerants) or/and cold-loving (psychrophiles) microorganisms. These microorganisms possess several structural and functional adaptations in order to perform normal life processes under the stressful low-temperature environments. Their biological activities maintain the nutrient flux in the environment and contribute to the global biogeochemical cycles. Limited culture-dependent and culture-independent studies have revealed their diversity in community structure and functional potential. Apart from the ecological importance, these microorganisms have been recognized as source of cold-active enzymes and novel bioactive compounds of industrial and biotechnological importance. Being an important part of the cryosphere, Himalaya needs to be explored at different dimensions related to the life of the inhabiting extremophiles. The present review discusses the distinct facts associated with microbial ecology from the Himalayan cryosphere perspective.