Microbiology of Lonar Lake and other soda lakes

Archaeal and Bacterial Communities Within the Wetland Alkaline Har Lake of the Qinghai-Xizang Plateau

Har Lake (HL) is in the northeastern basin of the Qinghai-Xizang Plateau (QTP), sits at an altitude of 4379 m, and is classified as a soda lake within a wetland ecosystem. Evaluating the archaeal and bacterial communities in HL could offer valuable insights into the biogeochemical cycling within plateau wetland lakes. Consequently, high-throughput sequencing of 16S rRNA genes was conducted in this study to assess the composition of HL microbial communities and their association with environmental factors. The HL archaeal communities comprised 5 phyla, 5 classes, and 30 genera, while the bacterial communities comprised 28 phyla, 52 classes, and 542 genera. The dominant archaeal phylum was Thaumarchaeota (30.30-93.07% relative abundances), followed by Woesearchaeota (6.79-67.78%), while the most abundant genus was Nitrososphaera (30.30-93.07%). The distribution of Nitrososphaera was significantly correlated with TN, Mg2+, and Ca2+ concentrations. Bacterial communities predominantly comprised the Proteobacteria phylum (59.33-74.70%), followed by Bacteroidetes (13.92-19.19%) and Firmicutes (0.69-9.60%). Dominant bacterial genera included halophilic hydrocarbon-degrading bacteria like Oleibacter (1.90-18.69%), Perlucidibaca (5.19-17.46%), and Thalassolituus (0.80-11.98%). The results suggest Nitrososphaera and Woesearchaeota may be key taxa involved in carbon and nitrogen biogeochemical cycling within HL. Additionally, the high abundances of halophilic hydrocarbon-degrading bacteria suggests that potential contamination of HL may have occurred due to frequent animal and human activities. Overall, this study provides valuable insights into the archaeal and bacterial community structures in high-altitude soda lake wetlands and their interactions with their unique environments.

Natronorarus salvus gen. nov., sp. nov., Halalkalicoccus ordinarius sp. nov., and Halalkalicoccus salilacus sp. nov., halophilic archaea from a soda lake and two saline lakes, and proposal to classify the genera Halalkalicoccus and Natronorarus into Halalkalicoccaceae fam. nov. in the order Halobacteriales within the class Halobacteria

Four novel halophilic archaeal strains CGA53T, CG83T, FCH27T, and SEDH24 were isolated from a soda lake and two saline lakes in China, respectively. Strain CGA53T showed the highest 16S rRNA gene similarity (92.6%) to Salinilacihabitans rarus AD-4T, and the other three strains were found to be related to Halalkalicoccus species with similarities of 97.6-98.3%. Metagenomic studies indicated that these four strains are low abundant inhabitants detected in these hypersaline environments, and only one MAG of Chagannuoer Soda Lake (CG) could be assigned to the genus Halalkalicoccus. Their growth occurred at 20-60 °C (optima, 42, 37, 37-42, and 35 °C), 0.9-5.1 M NaCl (optima, 3.9, 2.6, 3.5, and 3 M), and 0-1.0 M MgCl2 (optima, 0.5, 0.7, and 0.1) and pH 5.5-10.5 (optima, 9.0, 7.5, 7.0, and 7.0), respectively. Phylogenetic and phylogenomic analyses revealed that strains CG83T, FCH27T, and SEDH24 cluster with the current species of the genus Halalkalicoccus, and strain CGA53T forms an independent branch separated from this genus. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values among strains CGA53T, CG83T, FCH27T, SEDH24, and the type species of the current genera within the class Halobacteria were 67.4-81.6%, 16.5-28.6% and 49.7-74.1%, respectively, clearly lower than the cutoff values for species demarcation. Strain CGA53T may represent a novel species of a new genus according to the cutoff value for genus demarcation of 65% AAI. Diverse differential phenotypic characteristics, such as nutrition, biochemical activities, antibiotic sensitivity, and H2S formation, were found among these four strains and Halalkalicoccus species. Genome-based classification supported that strains CGA53T, CG83T, FCH27T, SEDH24, and the current species of Halalkalicoccus represent a novel family of the order Halobacteriales within the class Halobacteria.

Ecology and biogeochemistry of the microbial underworld in two sister soda lakes

BACKGROUND

Approximately 3.7 billion years ago, microbial life may have emerged in phosphate-rich salty ponds. Surprisingly, analogs of these environments are present in alkaline lake systems, recognized as highly productive biological ecosystems. In this study, we investigate the microbial ecology of two Canadian soda lake sediment systems characterized by naturally high phosphate levels.

RESULTS

Using a comprehensive approach involving geochemistry, metagenomics, and amplicon sequencing, we discovered that groundwater infiltration into Lake Goodenough sediments supported stratified layers of microbial metabolisms fueled by decaying mats. Effective degradation of microbial mats resulted in unexpectedly low net productivity. Evaporation of water from Last Chance Lake and its sediments led to saturation of brines and a habitat dominated by inorganic precipitation reactions, with low productivity, low organic matter turnover and little biological uptake of phosphorus, leading to high phosphate concentrations. Highly alkaline brines were found to be dominated by potentially dormant spore-forming bacteria. These saturated brines also hosted potential symbioses between Halobacteria and Nanoarchaeaota, as well as Lokiarchaea and bacterial sulfate reducers. Metagenome-assembled genomes of Nanoarchaeaota lacked strategies for coping with salty brines and were minimal for Lokiarchaea.

CONCLUSIONS

Our research highlights that modern analogs for origin-of-life conditions might be better represented by soda lakes with low phosphate concentrations. Thus, highly alkaline brine environments could be too extreme to support origin of life scenarios. These findings shed light on the complex interplay of microbial life in extreme environments and contribute to our understanding of early Earth environments.

Microbial nitrogen nutrition links to dissolved organic matter properties in East African lakes

East African lakes, especially soda lakes, are home habitats for massive numbers of wildlife such as flamingos, mammals, and fishes. These lakes are known for their high primary production due to local high temperatures, light intensities, and alkalinity (inorganic carbon). However, these lakes, normally within remote areas, receive low nutrient inputs. Ammonium (NH4+) recycling and/or nitrogen fixation can become the major N supply mechanisms for phytoplankton. However, the driving forces on microbial N nutrition in lakes with minimal anthropogenic disturbance remain poorly understood. Using stable isotope tracer techniques, NH4+ recycling rates were measured in 18 lakes and reservoirs in East Africa (Tanzania and Kenya) during the dry season in early 2020. Three functional genes (nifH, gdh, and ureC) relating to microbial N nutrition were also measured. The regeneration of NH4+ supported up to 71 % of the NH4+ uptake. Positive community biological NH4+ demands (CBAD) for all lakes and reservoirs indicate an obvious N demand from microbial community. Our study provides clear evidence that microbial NH4+ uptake rates linked closely to the dissolved organic matter (DOM) properties (e.g., the absorption coefficient at 254 nm, percents of total fluorescence intensity contributed by microbial humic-like and protein-like components) and that water residence time drives microbial NH4+ recycling by regulating the duration of in-lake DOM processing and influencing algal growth. Phytoplankton, especially those of Cyanophyceae, showed maximum biomass and higher NH4+ recycling rates at a certain range of water residence time (e.g., 5-8 years). However, CBAD showed a decreasing trend with longer water residence time, which may be influenced by changes in the algal community composition (e.g., % Cyanophyceae vs. % Bacillariophyceae). These results indicate that DOM dynamics and the water residence time have the potential to facilitate the understanding of microbial nitrogen supply status in East African lakes.

Spatiotemporal structure and composition of the microbial communities in hypersaline Lake Magadi, Kenya

Background

Soda lakes are habitats characterized by haloalkaline conditions also known to host unique microbial communities. The water chemistry changes with seasons due to evaporative concentration or floods from the surrounding grounds. However, it is not yet clear if the change in physiochemical changes influences the spatiotemporal diversity and structure of microbial communities in these ecosystems.

Methods

Using 16S rRNA gene amplicon sequencing, we investigated the diversity and structure of microbial communities in water and brine samples taken from Lake Magadi between June and September 2018. Additionally, physicochemical parameters were also analyzed for every sampling site. Additionally, physicochemical parameters were also analyzed for every sampling site.

Results

The abundant bacterial phyla were Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Verrumicrobia, Deinococcus-Thermus, Spirochaetes, and Chloroflexi. The Archaeal diversity was represented by phyla Euryachaeota, Crenarchaeota, Euryarchaeota, and Thaumarchaeota. The dominant bacterial species were: Euhalothece sp. (10.3%), Rhodobaca sp. (9.6%), Idiomarina sp. (5.8%), Rhodothermus sp. (3.0%), Roseinatronobacter sp. (2.4%), Nocardioides sp. (2.3%), Gracilimonas sp. (2.2%), and Halomonas sp. (2%). The dominant archaeal species included Halorubrum sp. (18.3%), Salinarchaeum sp. (5.3%), and Haloterrigena sp. (1.3%). The composition of bacteria was higher than that of archaea, while their richness and diversity varied widely across the sampling seasons. The α-diversity indices showed that high diversity was recorded in August, followed by September, June, and July in that order. The findings demonstrated that temperature, pH, P+, K+, NO3 -, and total dissolved solids (TDS) contributed majorly to the diversity observed in the microbial community. Multivariate analysis revealed significant spatial and temporal effects on β-diversity and salinity and alkalinity were the major drivers of microbial composition in Lake Magadi.

Conclusions

We provide insights into the relationships between microbial structure and geochemistry across various sampling sites in Lake Magadi.

Response of the metabolic activity and taxonomic composition of bacterial communities to mosaically varying soil salinity and alkalinity

Soil salinity and sodicity is a worldwide problem that affects the composition and activity of bacterial communities and results from elevated salt and sodium contents. Depending on the degree of environmental pressure and the combined effect of other factors, haloalkalitolerant and haloalkaliphilic bacterial communities will be selected. These bacteria play a potential role in the maintenance and restoration of salt-affected soils; however, until recently, only a limited number of studies have simultaneously studied the bacterial diversity and activity of saline-sodic soils. Soil samples were collected to analyse and compare the taxonomic composition and metabolic activity of bacteria from four distinct natural plant communities at three soil depths corresponding to a salinity‒sodicity gradient. Bacterial diversity was detected using 16S rRNA gene Illumina MiSeq amplicon sequencing. Community-level physiological profiles (CLPPs) were analysed using the MicroResp™ method. The genus-level bacterial composition and CLPPs differed significantly in soils with different alkaline vegetation. The surface soil samples also significantly differed from the intermediate and deep soil samples. The results showed that the pH, salt content, and Na+ content of the soils were the main edaphic factors influencing both bacterial diversity and activity. With salinity and pH, the proportion of the phylum Gemmatimonadota increased, while the proportions of Actinobacteriota and Acidobacteriota decreased.

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.

Alkaliphilic/Alkali-Tolerant Fungi: Molecular, Biochemical, and Biotechnological Aspects

Biotechnologist interest in extremophile microorganisms has increased in recent years. Alkaliphilic and alkali-tolerant fungi that resist alkaline pH are among these. Alkaline environments, both terrestrial and aquatic, can be created by nature or by human activities. Aspergillus nidulans and Saccharomyces cerevisiae are the two eukaryotic organisms whose pH-dependent gene regulation has received the most study. In both biological models, the PacC transcription factor activates the Pal/Rim pathway through two successive proteolytic mechanisms. PacC is a repressor of acid-expressed genes and an activator of alkaline-expressed genes when it is in an active state. It appears, however, that these are not the only mechanisms associated with pH adaptations in alkali-tolerant fungi. These fungi produce enzymes that are resistant to harsh conditions, i.e., alkaline pH, and can be used in technological processes, such as in the textile, paper, detergent, food, pharmaceutical, and leather tanning industries, as well as in bioremediation of pollutants. Consequently, it is essential to understand how these fungi maintain intracellular homeostasis and the signaling pathways that activate the physiological mechanisms of alkali resistance in fungi.

Habitat distribution of the genus Belliella in continental waters and the description of Belliella alkalica sp. nov., Belliella calami sp. nov. and Belliella filtrata sp. nov

The genus Belliella belongs to the family Cyclobacteriaceae (order Cytophagales, phylum Bacteroidota) and harbours aerobic chemoheterotrophic bacteria. Members of this genus were isolated from various aquatic habitats, and our analysis based on global amplicon sequencing data revealed that their relative abundance can reach up to 5-10 % of the bacterioplankton in soda lakes and pans. Although a remarkable fraction of the most frequent genotypes that we identified from continental aquatic habitats is still uncultured, five new alkaliphilic Belliella strains were characterized in detail in this study, which were isolated from three different soda lakes and pans of the Carpathian Basin (Hungary). Cells of all strains were Gram-stain-negative, obligate aerobic, rod-shaped, non-motile and non-spore-forming. The isolates were oxidase- and catalase-positive, red-coloured, but did not contain flexirubin-type pigments; they formed bright red colonies that were circular, smooth and convex. Their major isoprenoid quinone was MK-7 and the predominant fatty acids were iso-C_15 : 0, iso-C_17 : 0 3-OH and summed feature 3 containing C_16 : 1  ω6c and/or C_16 : 1  ω7c. The polar lipid profiles contained phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified glycolipid, and several unidentified lipids and aminolipids. Based on whole-genome sequences, the DNA G+C content was 37.0, 37.1 and 37.8 mol % for strains R4-6^T, DMA-N-10a^T and U6F3^T, respectively. The distinction of three new species was confirmed by in silico genomic comparison. Orthologous average nucleotide identity (<85.4 %) and digital DNA-DNA hybridization values (<38.9 %) supported phenotypic, chemotaxonomic and 16S rRNA gene sequence data and, therefore, the following three novel species are proposed: Belliella alkalica sp. nov. (represented by strains R4-6^T=DSM 111903^T=JCM 34281^T=UCCCB122^T and S4-10), Belliella calami sp. nov. (DMA-N-10a^T=DSM 107340^T=JCM 34280^T=UCCCB121^T) and Belliella filtrata sp. nov. (U6F3^T=DSM 111904^T=JCM 34282^T=UCCCB123^T and U6F1). Emended descriptions of species Belliella aquatica, Belliella baltica, Belliella buryatensis, Belliella kenyensis and Belliella pelovolcani are also presented.

Natronogracilivirga saccharolytica gen. nov., sp. nov. and Cyclonatronum proteinivorum gen. nov., sp. nov., haloalkaliphilic organotrophic bacteroidetes from hypersaline soda lakes forming a new family Cyclonatronaceae fam. nov. in the order Balneolales

Two heterotrophic bacteroidetes strains were isolated as satellites from autotrophic enrichments inoculated with samples from hypersaline soda lakes in southwestern Siberia. Strain Z-1702^T is an obligate anaerobic fermentative saccharolytic bacterium from an iron-reducing enrichment culture, while Ca. Cyclonatronum proteinivorum Omega^T is an obligate aerobic proteolytic microorganism from a cyanobacterial enrichment. Cells of isolated bacteria are characterized by highly variable morphology. Both strains are chloride-independent moderate salt-tolerant obligate alkaliphiles and mesophiles. Strain Z-1702^T ferments glucose, maltose, fructose, mannose, sorbose, galactose, cellobiose, N-acetyl-glucosamine and alpha-glucans, including starch, glycogen, dextrin, and pullulan. Strain Omega^T is strictly proteolytic utilizing a range of proteins and peptones. The main polar lipid fatty acid in both strains is iso-C_15:0, while other major components are various C₁₆ and C₁₇ isomers. According to pairwise sequence alignments using BLAST Gracilimonas was the nearest cultured relative to both strains (<90% of 16S rRNA gene sequence identity). Phylogenetic analysis placed strain Z-1702^T and strain Omega^T as two different genera in a deep-branching clade of the new family level within the order Balneolales with genus. Based on physiological characteristics and phylogenetic position of strain Z-1702^T it was proposed to represent a novel genus and species Natronogracilivirga saccharolityca gen. nov., sp. nov. (= DSMZ 109061^T =JCM 32930^T =VKM B 3262^T). Furthermore, phylogenetic and phenotypic parameters of N. saccharolityca and C. proteinivorum gen. nov., sp. nov., strain Omega^T (=JCM 31662^T, =UNIQEM U979^T), make it possible to include them into a new family with a proposed designation Cyclonatronaceae fam. nov..

Identification of environmental stress parameters to study the natural colour change of water in highly saline inland Crater Lake at Lonar, India

Lonar Lake is a highly saline inland water body created by a crater in Maharashtra, India. A rare occurrence of the colour change of lake water from green to brown and eventually to pinkish-red was observed in Lonar in June 2020. This phenomenon attracted the attention of researchers, academicians and interestingly legal fraternity to understand the causes of colour change. The literature studies coupled the phenomenon of colouration of water to three aspects: the presence of halophilic Halobacterium salinarum or an algal species of Dunaliella (Dunaliella salina) or oxidization of metals (Fe and Mn) present in water. A comprehensive study was done to understand and assess the change in the colour of Lonar Lake water. The green colour of the lake is primarily due to the dominance of chlorophyll-a pigment in the algae population. The stressed condition in June 2020 adversely affected the photosynthesis activity of Dunaliella sp. resulting in the red colouration of the species. This red colour of Dunaliella sp. is due to the formation of a pigment named carotenoid which is similar to that in halophilic bacteria. This pigment completely hides the green chloroplast, and water turns pinkish-red. This study describes detailed investigations of environmental and climatic parameters to determine possible causes of abiotic stress on the algae population of the lake. The major factors contributing to the stressed conditions are high dissolved solids, alkalinity and alkaline pH due to salts in the lake water due to evaporation losses and limited rainfall over the months. The study further verified whether the colour change is a cyclic event and predicted possible lake conditions for the event of colour change to occur in the future.

High exogenous humus inhibits greenhouse gas emissions from steppe lakes

Although freshwater lakes are considered to be an important source of greenhouse gas (GHG) emissions, the potential driving mechanisms of such emissions are not well understood, especially in steppe lakes. In this study, the GHG emission characteristics in Hulun Lake Basin, including Hulun Lake, Beier Lake, Wulannuoer Lake, and their surrounding watersheds were investigated. The average methane (CH₄) and nitrous oxide (N₂O) emission fluxes released from rivers were 67.84 ± 20.53 and 0.11 ± 0.04 μg m^-2·min^-1, which were larger than those of lakes, with values of 28.60 ± 13.02 and 0.06 ± 0.02 μg m^-2·min^-1, respectively. Conversely, the average carbon dioxide (CO₂) emission flux from lakes (1816.58 ± 498.98 μg m^-2·min^-1) was higher than that of rivers of (1795.41 ± 670.49 μg m^-2·min^-1). The water in Hulun Lake Basin was rich in organic matter and had a high chemical oxygen demand (COD). Three-dimensional fluorescence combined with a parallel factor analysis (3D-EEM-PARAFAC) demonstrated that the organic matter was composed of four humus types (from Component 1 (C1) to Component 4 (C4)), of which, C1 and C4 were terrestrial humus. The fluorescence index (FI) and humification index (HIX) indicated that the organic matter in the water was mainly imported from exogenous humus. The GHG emission fluxes were negatively correlated with these four components, indicating that GHG emissions were mainly affected by the organic matter source and components, and humus was the most important factor that inhibited GHG emissions in steppe lakes. However, the GHG emission flux was relatively high in some areas of the lake, especially in areas with high nutrient levels or where algal blooms occurred, as evidenced by the significantly positive correlations with total nitrogen (TN), total phosphorous (TP), and chlorophyll-a (chl-a) (p < 0.01). The algae-derived organic matter simulated the decomposition of refractory humus, thus, promoting GHG emissions. These findings are crucial for accurately evaluating the GHG emission fluxes, understanding the carbon cycle, and proposing future management strategies for steppe lakes.

Discovery of novel carbohydrate degrading enzymes from soda lakes through functional metagenomics

Extremophiles provide a one-of-a-kind source of enzymes with properties that allow them to endure the rigorous industrial conversion of lignocellulose biomass into fermentable sugars. However, the fact that most of these organisms fail to grow under typical culture conditions limits the accessibility to these enzymes. In this study, we employed a functional metagenomics approach to identify carbohydrate-degrading enzymes from Ethiopian soda lakes, which are extreme environments harboring a high microbial diversity. Out of 21,000 clones screened for the five carbohydrate hydrolyzing enzymes, 408 clones were found positive. Cellulase and amylase, gave high hit ratio of 1:75 and 1:280, respectively. A total of 378 genes involved in the degradation of complex carbohydrates were identified by combining high-throughput sequencing of 22 selected clones and bioinformatics analysis using a customized workflow. Around 41% of the annotated genes belonged to the Glycoside Hydrolases (GH). Multiple GHs were identified, indicating the potential to discover novel CAZymes useful for the enzymatic degradation of lignocellulose biomass from the Ethiopian soda Lakes. More than 73% of the annotated GH genes were linked to bacterial origins, with Halomonas as the most likely source. Biochemical characterization of the three enzymes from the selected clones (amylase, cellulase, and pectinase) showed that they are active in elevated temperatures, high pH, and high salt concentrations. These properties strongly indicate that the evaluated enzymes have the potential to be used for applications in various industrial processes, particularly in biorefinery for lignocellulose biomass conversion.

Occurrence of methane-oxidizing bacteria and methanogenic archaea in earth’s cave systems—A metagenomic analysis

Karst ecosystems represent up to 25% of the land surface and recent studies highlight their potential role as a sink for atmospheric methane. Despite this, there is limited knowledge of the diversity and distribution of methane-oxidizing bacteria (MOB) or methanogens in karst caves and the sub-surface environment in general. Here, we performed a survey of 14 shotgun metagenomes from cave ecosystems covering a broad set of environmental conditions, to compare the relative abundance and phylogenetic diversity of MOB and methanogens, targeting biomarker genes for methane monooxygenase (pmoA and mmoX) and methyl-coenzyme M reductase (mcrA). Taxonomic analysis of metagenomes showed 0.02–1.28% of classified reads were related to known MOB, of which Gammaproteobacterial MOB were the most abundant making up on average 70% of the surveyed caves’ MOB community. Potential for biogenic methane production in caves was also observed, with 0.008–0.39% of reads classified to methanogens and was dominated by sequences related to Methanosarcina. We have also generated a cave ecosystems protein database (CEPD) based on protein level assembly of cave metagenomes that can be used to profile genes of interest.

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.

A comprehensive evaluation of organic micropollutants (OMPs) pollution and prioritization in equatorial lakes from mainland Tanzania, East Africa

A lack of understanding the fate of highly toxic organic micropollutants (OMPs) in the equatorial lakes of Tanzania hinders public awareness for protecting these unique aquatic ecosystems, which are precious water resources and stunning wildlife habitats. To address this knowledge gap, the occurrence of 70 anthropogenically-sourced OMPs, including phthalates (PAEs), polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs), was investigated in the water and sediment of 18 lakes in Tanzania. Similar residue concentrations were found in both compartments, showing higher pollution of PAEs ranging from 835.0 to 13,153.1 ng/L in water and 244.6-8691.8 ng/g dw in sediment, followed by PAHs, while OCPs and PCBs were comparatively lower. According to the multi-criteria scoring method for prioritization, the final OMP priority list for the lake environment in Tanzania comprised 25 chemicals, specifically 5 PAEs (DEHP, DIBP, DBP, DCHP and DMPP), 6 PCBs (PCB153, PCB105, PCB28, PCB156, PCB157 and PCB167), 6 PAHs (BaP, BaA, BbF, Pyr, DahA and InP) and 8 OCPs (cis-chlordane, trans-chlordane, p,p'-DDD, p,p'-DDE, p,p'-DDT, endrin, methoxychlor and heptachlor epoxide), suggesting the key substances for conventional monitoring and pollution control in these equatorial lakes, with an emphasis on PAEs, especially DEHP, due to the top priority and endocrine disruptor properties.

Deep Subsurface Hypersaline Environment as a Source of Novel Species of Halophilic Sulfur-Oxidizing Bacteria

The sulfur cycle participates significantly in life evolution. Some facultatively autotrophic microorganisms are able to thrive in extreme environments with limited nutrient availability where they specialize in obtaining energy by oxidation of reduced sulfur compounds. In our experiments focused on the characterization of halophilic bacteria from a former salt mine in Solivar (Presov, Slovakia), a high diversity of cultivable bacteria was observed. Based on ARDRA (Amplified Ribosomal DNA Restriction Analysis), at least six groups of strains were identified with four of them showing similarity levels of 16S rRNA gene sequences lower than 98.5% when compared against the GenBank rRNA/ITS database. Heterotrophic sulfur oxidizers represented ~34% of strains and were dominated by Halomonas and Marinobacter genera. Autotrophic sulfur oxidizers represented ~66% and were dominated by Guyparkeria and Hydrogenovibrio genera. Overall, our results indicate that the spatially isolated hypersaline deep subsurface habitat in Solivar harbors novel and diverse extremophilic sulfur-oxidizing bacteria.

Metagenomic insights into the environmental adaptation and metabolism of Candidatus Haloplasmatales, one archaeal order thriving in saline lakes

The KTK 4A-related Thermoplasmata thrives in the sediment of saline lakes; however, systematic research on its taxonomy, environmental adaptation and metabolism is lacking. Here, we detected this abundant lineage in the sediment of five artificially separated ponds (salinity 7.0%-33.0%) within a Chinese soda-saline lake using culture-independent metagenomics and archaeal 16S rRNA gene amplicons. The phylogenies based on the 16S rRNA gene, and 122 archaeal ubiquitous single-copy proteins and genome-level identity analyses among the metagenome-assembled genomes demonstrate this lineage forming a novel order, Candidatus Haloplasmatales, comprising four genera affiliated with the identical family. Isoelectric point profiles of predicted proteomes suggest that most members adopt the energetically favourable 'salt-in' strategy. Functional prediction indicates the lithoheterotrophic nature with the versatile metabolic potentials for carbohydrate and organic acids as well as carbon monoxide and hydrogen utilization. Additionally, hydrogenase genes hdrABC-mvhADG are linked with incomplete reductive citrate cycle genes in the genomes, suggesting their functional connection. Comparison with the coupling of HdrABC-MvhADG and methanogenesis pathway provides new insights into the compatibility of laterally acquired methanogenesis with energy metabolism in the related order Methanomassiliicoccales. Globally, our research sheds light on the taxonomy, environmental adaptative mechanisms, metabolic potentials and evolutional significance of Ca. Haloplasmatales.

Diversity and Metabolism of Microbial Communities in a Hypersaline Lake along a Geochemical Gradient

In the south of western Siberia (Russia), there are many unique and unexplored soda, saline, and freshwater lakes. In this study, the results are presented on microbial diversity, its metabolic potential, and their relation with a set of geochemical parameters for a hypersaline lake ecosystem in the Novosibirsk region (Oblast). The metagenomic approach used in this work allowed us to determine the composition and structure of a floating microbial community, the upper layer of silt, and the strata of bottom sediments in a natural saline lake via two bioinformatic approaches, whose results are in good agreement with each other. In the floating microbial community and in the upper layers of the bottom sediment, bacteria of the Proteobacteria (Gammaproteobacteria), Cyanobacteria, and Bacteroidetes phyla were found to predominate. The lower layers were dominated by Proteobacteria (mainly Deltaproteobacteria), Gemmatimonadetes, Firmicutes, and Archaea. Metabolic pathways were reconstructed to investigate the metabolic potential of the microbial communities and other hypothetical roles of the microbial communities in the biogeochemical cycle. Relations between different taxa of microorganisms were identified, as was their potential role in biogeochemical transformations of C, N, and S in a comparative structural analysis that included various ecological niches.

Microbial diversity in extreme environments

A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.

Salt tolerance-based niche differentiation of soil ammonia oxidizers

Ammonia oxidizers are key players in the global nitrogen cycle, yet little is known about their ecological performances and adaptation strategies for growth in saline terrestrial ecosystems. This study combined ¹³C-DNA stable-isotope probing (SIP) microcosms with amplicon and shotgun sequencing to reveal the composition and genomic adaptations of active ammonia oxidizers in a saline-sodic (solonetz) soil with high salinity and pH (20.9 cmol_c exchangeable Na⁺ kg^-1 soil and pH 9.64). Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) exhibited strong nitrification activities, although AOB performed most of the ammonia oxidation observed in the solonetz soil and in the farmland soil converted from solonetz soil. Members of the Nitrosococcus, which are more often associated with aquatic habitats, were identified as the dominant ammonia oxidizers in the solonetz soil with the first direct labeling evidence, while members of the Nitrosospira were the dominant ammonia oxidizers in the farmland soil, which had much lower salinity and pH. Metagenomic analysis of "Candidatus Nitrosococcus sp. Sol14", a new species within the Nitrosococcus lineage, revealed multiple genomic adaptations predicted to facilitate osmotic and pH homeostasis in this extreme habitat, including direct Na⁺ extrusion/H⁺ import and the ability to increase intracellular osmotic pressure by accumulating compatible solutes. Comparative genomic analysis revealed that variation in salt-tolerance mechanisms was the primary driver for the niche differentiation of ammonia oxidizers in saline-sodic soils. These results demonstrate how ammonia oxidizers can adapt to saline-sodic soil with excessive Na⁺ content and provide new insights on the nitrogen cycle in extreme terrestrial ecosystems.

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.

Microbial community of soda Lake Van as obtained from direct and enriched water, sediment and fish samples

Soda lakes are saline and alkaline ecosystems that are considered to have existed since the first geological records of the world. These lakes support the growth of ecologically and economically important microorganisms due to their unique geochemistry. Microbiota members of lakes are valuable models to study the link between community structure and abiotic parameters such as pH and salinity. Lake Van is the largest endroheic lake and in this study, bacterial diversity of lake water, sediment, and pearl mullet (inci kefali; Alburnus tarichi), an endemic species of fish which are collected from different points of the lake, are studied directly and investigated meticulously using a metabarcoding approach after pre-enrichment. Bacterial community structures were identified using Next Generation Sequencing of the 16S rRNA gene. The analysis revealed that the samples of Lake Van contain high level of bacterial diversity. Direct water samples were dominated by Proteobacteria, Cyanobacteria, and Bacteroidota, on the other hand, pre-enriched water samples were dominated by Proteobacteria and Firmicutes at phylum-level. In direct sediment samples Proteobacteria, whereas in pre-enriched sediment samples Firmicutes and Proteobacteria were determined at highest level. Pre-enriched fish samples were dominated by Proteobacteria and Firmicutes at phylum-level. In this study, microbiota members of Lake Van were identified by taxonomic analysis.

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

Extended divergence estimates and species descriptions of new craspedid choanoflagellates from the Atacama Desert, Northern Chile

In contrast to previous perspectives, hypersaline environments have been proven to harbour a variety of potentially highly adapted microorganisms, in particular unicellular eukaryotes. The isolated, hypersaline waterbodies in the Atacama Desert, Northern Chile are exposed to high UV radiation and deposition of toxic heavy metals, making them of great interest regarding studies on speciation and evolutionary processes. In the past two years, among a variety of other protist species, five new species of heterotrophic choanoflagellates were described and analysed from this area, showing an adaptation to a broad range of salinities. Morphological data alone does not allow for species delineation within craspedid species, additional molecular data is essential for modern taxonomy. In addition, molecular clock analyses pointed towards a strong selection force of the extreme environmental conditions. Within this study, we describe three additional craspedid choanoflagellate species, isolated from different aquatic environments. Phylogenetic analyses show two distinct clades of choanoflagellates from the Atacama, suggesting two independent invasions of at least two ancestral marine species, and, as indicated by our new data, a possible dispersal by Andean aquifers. The extended molecular clock analysis based on transcriptomic data of choanoflagellate strains from the Salar de Llamará, a hypersaline basin within the Central Depression of the Atacama Desert, reflects colonisation and divergence events which correspond to geological data of the paleohydrology.

Long term natural restoration creates soil‐like microbial communities in bauxite residue: A 50‐year filed study

Ecological reconstruction on bauxite residue (tailings) disposal areas is regarded as an effective approach to eliminate potential environmental risks. Establishment of microbial communities and associated functions may improve physical and chemical properties, and may stimulate soil formation in bauxite residue. Spontaneous colonization at a disposal area in Shandong Province, China, over 50 years, indicated that natural weathering can ameliorate residues, and in turn, support the establishment of vegetation communities. Residue samples were collected from unrestored, poorly restored and well restored areas to investigate the development of microbial communities and associated functions. Microbiota significantly developed after long term natural restoration. Microbial biomass, respiration and enzyme activities significantly increased in restored bauxite residue, whereas the metabolic quotient significantly decreased. In addition, the long‐term natural restoration significantly shaped the microbial structure from alkalophilic and halophilic assemblages (Firmicutes and Actinobacteria) to neutrophilic assemblages (Acidobacteria and Planctomycetes). Both microbial communities and associated functions in well restored residue had high similarity with that in natural soil, indicating that long term restoration created diverse soil‐like microbial communities and functions. Redundancy analysis (RDA) revealed that TN, followed by Na+, ESP, SOC, AP and pH were the major influence factors in the development of microbial communities in bauxite residue. These findings provide us a biogeochemical perspective to reveal soil formation in bauxite residue and suggest that nutrient supplement and regulation of salinity‐alkalinity may benefit for the establishment of microbial communities and functions in bauxite residue.

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.

Hydrogenotrophic Methanogenesis Under Alkaline Conditions

A cement-based geological disposal facility (GDF) is one potential option for the disposal of intermediate level radioactive wastes. The presence of both organic and metallic materials within a GDF provides the opportunity for both acetoclastic and hydrogenotrophic methanogenesis. However, for these processes to proceed, they need to adapt to the alkaline environment generated by the cementitious materials employed in backfilling and construction. Within the present study, a range of alkaline and neutral pH sediments were investigated to determine the upper pH limit and the preferred route of methane generation. In all cases, the acetoclastic route did not proceed above pH 9.0, and the hydrogenotrophic route dominated methane generation under alkaline conditions. In some alkaline sediments, acetate metabolism was coupled to hydrogenotrophic methanogenesis via syntrophic acetate oxidation, which was confirmed through inhibition studies employing fluoromethane. The absence of acetoclastic methanogenesis at alkaline pH values (>pH 9.0) is attributed to the dominance of the acetate anion over the uncharged, undissociated acid. Under these conditions, acetoclastic methanogens require an active transport system to access their substrate. The data indicate that hydrogenotrophic methanogenesis is the dominant methanogenic pathway under alkaline conditions (>pH 9.0).

Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira

Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospira distribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3-12.8 g salt/l), highly alkaline (pH 8.9-10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members from  Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, "Candidatus Nitrospira alkalitolerans", revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. "Ca. Nitrospira alkalitolerans" also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.

Grazing pressure-induced shift in planktonic bacterial communities with the dominance of acIII-A1 actinobacterial lineage in soda pans

Astatic soda pans of the Pannonian Steppe are unique environments with respect to their multiple extreme physical and chemical characteristics (high daily water temperature fluctuation, high turbidity, alkaline pH, salinity, polyhumic organic carbon concentration, hypertrophic state and special ionic composition). However, little is known about the seasonal dynamics of the bacterial communities inhabiting these lakes and the role of environmental factors that have the main impact on their structure. Therefore, two soda pans were sampled monthly between April 2013 and July 2014 to reveal changes in the planktonic community. By late spring in both years, a sudden shift in the community structure was observed, the previous algae-associated bacterial communities had collapsed, resulting the highest ratio of Actinobacteria within the bacterioplankton (89%, with the dominance of acIII-A1 lineage) ever reported in the literature. Before these peaks, an extremely high abundance (> 10,000 individuum l-1) of microcrustaceans (Moina brachiata and Arctodiaptomus spinosus) was observed. OTU-based statistical approaches showed that in addition to algal blooms and water-level fluctuations, zooplankton densities had the strongest effect on the composition of bacterial communities. In these extreme environments, this implies a surprisingly strong, community-shaping top-down role of microcrustacean grazers.

Bacterial Communities Associated with the Biofilms Formed in High-Altitude Brackish Water Pangong Tso Located in the Himalayan Plateau

Pangong Tso is a long and narrow lake situated at an altitude of ~ 4266 m amsl in the Himalayan Plateau on the side of the India/China border. Biofilm has been observed in a small area near the shore of Pangong Tso. Bacterial communities of the lake sediment, water and biofilms were studied using amplicon sequencing of V3-V4 region of the 16S rRNA gene. The standard QIIME pipeline was used for analysis. The metabolic potential of the community was predicted using functional prediction tool Tax4Fun. Bacterial phyla Proteobacteria, followed by Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria, and Firmicutes, were found to be dominant across these samples. Shannon's and Simpson's alpha diversity analysis revealed that sediment communities are the most diverse, and water communities are the least diverse. Principal Coordinates based beta diversity analysis showed significant variation in the bacterial communities of the water, sediment and biofilm samples. Bacterial phyla Verrucomicrobia, Deinococcus-Thermus and Cyanobacteria were explicitly enriched in the biofilm samples. Predictive functional profiling of these bacterial communities showed a higher abundance of genes involved in photosynthesis, biosynthesis of secondary metabolites, carbon fixation in photosynthetic organisms and glyoxylate and dicarboxylate metabolism in the biofilm sample. In conclusion, the Pangong Tso bacterial communities are quite similar to other saline and low-temperature lakes in the Tibetan Plateau. Bacterial community structure of the biofilm samples was significantly different from that of the water and sediment samples and enrichment of saprophytic communities was observed in the biofilm samples, indicating an important succession event in this high-altitude lake.

Abundant Taxa and Favorable Pathways in the Microbiome of Soda-Saline Lakes in Inner Mongolia

Soda-saline lakes are a special type of alkaline lake in which the chloride concentration is greater than the carbonate/bicarbonate concentration. Due to the high pH and a usually higher osmotic pressure than that of a normal soda lake, the microbes may need more energy to thrive in such a double-extreme environment. In this study, we systematically investigated the microbiome of the brine and sediment samples of nine artificially separated ponds (salinities from 5.5% to saturation) within two soda-saline lakes in Inner Mongolia of China, assisted by deep metagenomic sequencing. The main inorganic ions shaped the microbial community in both the brines and sediments, and the chloride concentration exhibited the most significant effect. A total of 385 metagenome-assembled genomes (MAGs) were generated, in which 38 MAGs were revealed as the abundant species in at least one of the eighteen different samples. Interestingly, these abundant species also represented the most branches of the microbiome of the soda-saline lakes at the phylum level. These abundant taxa were close relatives of microorganisms from classic soda lakes and neutral saline environments, but forming a combination of both habitats. Notably, approximately half of the abundant MAGs had the potential to drive dissimilatory sulfur cycling. These MAGs included four autotrophic Ectothiorhodospiraceae MAGs, one Cyanobacteria MAG and nine heterotrophic MAGs with the potential to oxidize sulfur, as well as four abundant MAGs containing genes for elemental sulfur respiration. The possible reason is that reductive sulfur compounds could provide additional energy for the related species, and reductions of oxidative sulfur compounds are more prone to occur under alkaline conditions which support the sulfur cycling. In addition, a unique 1,4-alpha-glucan phosphorylation pathway, but not a normal hydrolysis one, was found in the abundant Candidatus Nanohaloarchaeota MAG NHA-1, which would produce more energy in polysaccharide degradation. In summary, this work has revealed the abundant taxa and favorable pathways in the soda-saline lakes, indicating that efficient energy regeneration pathway may increase the capacity for environmental adaptation in such saline-alkaline environments. These findings may help to elucidate the relationship between microbial metabolism and adaptation to extreme environments.

The dynamic development of bacterial community following long-term weathering of bauxite residue

Bauxite residue is the industrial waste generated from alumina production and commonly deposited in impoundments. These sites are bare of vegetation due to the extreme high salinity and alkalinity, as well as lack of nutrients. However, long term weathering processes could improve residue properties to support the plant establishment. Here we investigate the development of bacterial communities and the geochemical drivers in bauxite residue, using Illumina high-throughput sequencing technology. Long term weathering reduced the pH in bauxite residue and increased its nutrients content. The bacterial community also significantly developed during long term weathering processes. Taxonomic analysis revealed that natural weathering processes encouraged the populations of Proteobacteria, Chloroflexi, Acidobacteria and Planctomycetes, whereas reducing the populations of Firmicutes and Actinobacteria. Redundancy analysis (RDA) indicated that total organic carbon (TOC) was the dominant factors affecting microbial structure. The results have demonstrated that natural weathering processes improved the soil development on the abandoned bauxite residue disposal areas, which also increased our understanding of the correlation between microbial variation and residue properties during natural weathering processes in Bauxite residue disposal areas.

Cultivation of Diverse Microorganisms from Hypersaline Lake and Impact of Delay in Sample Processing on Cell Viability

The Sambhar Salt Lake is a halite rich athalassohaline basin, provides a unique opportunity for microbial ecologists to study halophiles. The lake has a high proportion of Na⁺ and Cl^- ions making it a hypersaline ecosystem. In the current study, archaea and bacteria from Sambhar Lake were isolated using two cultivation approaches. A total of 449 isolates were obtained, out of which 13 represent archaeal while 12 represent bacterial genera. Natronococcus and Alkalibacillus were found predominant groups among archaea and bacteria, respectively. Apart from the common genera in both the approaches Alteribacillus, Halobacillus, Halorubrum, Lentibacillus, Natronorubrum, Piscibacillus and Thalassobacillus were found only in the samples processed onsite however only three genera Aliidiomarina, Natrinema and Natronolimnobius were isolated when samples were processed in the laboratory after transportation using the same growth conditions. Other than the isolation of diverse group of organisms 13 putative novel taxa with similarity less than 98% were identified using 16S rRNA gene sequencing.

Reconditioning Degraded Mine Site Soils With Exogenous Soil Microbes: Plant Fitness and Soil Microbiome Outcomes

Mining of mineral resources substantially alters both the above and below-ground soil ecosystem, which then requires rehabilitation back to a pre-mining state. For belowground rehabilitation, recovery of the soil microbiome to a state which can support key biogeochemical cycles, and effective plant colonization is usually required. One solution proposed has been to translate microbial inocula from agricultural systems to mine rehabilitation scenarios, as a means of reconditioning the soil microbiome for planting. Here, we experimentally determine both the aboveground plant fitness outcomes and belowground soil microbiome effects of a commercially available soil microbial inocula (SMI). We analyzed treatment effects at four levels of complexity; no SMI addition control, Nitrogen addition alone, SMI addition and SMI plus Nitrogen addition over a 12-week period. Our culture independent analyses indicated that SMIs had a differential response over the 12-week incubation period, where only a small number of the consortium members persisted in the semi-arid ecosystem, and generated variable plant fitness responses, likely due to plant-microbiome physiological mismatching and low survival rates of many of the SMI constituents. We suggest that new developments in custom-made SMIs to increase rehabilitation success in mine site restoration are required, primarily based upon the need for SMIs to be ecologically adapted to both the prevailing edaphic conditions and a wide range of plant species likely to be encountered.

Dual bloom of green algae and purple bacteria in an extremely shallow soda pan

In April 2014, dual bloom of green algae and purple bacteria occurred in a shallow, alkaline soda pan (Kiskunság National Park, Hungary). The water was only 5 cm deep, in which an upper green layer was clearly separated from a near-sediment purple one. Based on microscopy and DNA-based identification, the upper was inhabited by a dense population of the planktonic green alga, Oocystis submarina Lagerheim, while the deeper layer was formed by purple, bacteriochlorophyll-containing bacteria, predominated by Thiorhodospira and Rhodobaca. Additional bacterial taxa with a presumed capability of anoxygenic phototrophic growth belonged to the genera Loktanella and Porphyrobacter. Comparing the bacterial community of the purple layer with a former blooming event in a nearby soda pan, similar functional but different taxonomic composition was revealed. Members from many dominant bacterial groups were successfully cultivated including potentially new species, which could be the result of the application of newly designed media.

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.

The Complex Nature of Tupanviruses

The discovery of giant viruses revealed a new level of complexity in the virosphere, raising important questions about the diversity, ecology, and evolution of these viruses. The family Mimiviridae was the first group of amoebal giant viruses to be discovered (by Bernard La Scola and Didier Raoult team), containing viruses with structural and genetic features that challenged many concepts of classic virology. The tupanviruses are among the newest members of this family and exhibit structural, biological, and genetic features never previously observed in other giant viruses. The complexity of these viruses has put us one step forward toward the comprehension of giant virus biology and evolution, but also has raised important questions that still need to be addressed. In this chapter, we tell the history behind the discovery of one of the most complex viruses isolated to date, highlighting the unique features exhibited by tupanviruses, and discuss how these giant viruses have contributed to redefining limits for the virosphere.

Phenotypic and Genomic Properties of a Novel Deep-Lineage Haloalkaliphilic Member of the Phylum Balneolaeota From Soda Lakes Possessing Na+-Translocating Proteorhodopsin

Stable development of a heterotrophic bacterial satellite with a peculiar cell morphology has been observed in several enrichment cultures of haloalkaliphilic benthic filamentous cyanobacteria from a hypersaline soda lake in Kulunda Steppe (Altai, Russia). The organism was isolated in pure culture (strain Omega) using sonicated cyanobacterial cells as substrate and it was identified as a deep phylogenetic lineage within the recently proposed phylum Balneolaeota. It is an obligately aerobic heterotroph utilizing proteins and peptides for growth. The cell morphology significantly varied from semicircles to long filaments depending on the growth conditions. The cultures are red-orange colored due to a presence of carotenoids. The isolate is an obligate alkaliphile with a pH range for growth from 8.5 to 10.5 (optimum at 9.5-10) and moderately salt-tolerant with a range from 0.3 to 3 M total Na+ (optimum at 1 M). The genome analysis of strain Omega demonstrated a presence of gene, encoding a proteorhodopsin forming a separate branch in the sodium-translocating proteorhodopsin family. Experiments with washed cells of Omega confirmed light-dependent sodium export. A possible physiological role of the sodium proteorhodopsin in strain Omega is discussed. Phylogenomic analysis demostrated that strain Omega forms an deep, independent branch of a new genus and family level within a recently established phylum Balneolaeota.

Role of Extracellular Carbonic Anhydrase in Dissolved Inorganic Carbon Uptake in Alkaliphilic Phototrophic Biofilm

Alkaline Soda Lakes are extremely productive ecosystems, due to their high dissolved inorganic carbon (DIC) concentrations. Here, we studied the dynamics of the carbonate system, in particular, the role of extracellular carbonic anhydrase (eCA) of an alkaliphilic phototrophic biofilm composed of bacteria enriched from soda lake benthic mats. By using measurements with microsensors and membrane inlet mass spectrometry, combined with mathematical modeling, we show how eCA controls DIC uptake. In our experiments, the activity of eCA varied four-fold, and was controlled by the bicarbonate concentration during growth: a higher bicarbonate concentration led to lower eCA activity. Inhibition of eCA decreased both the net and the gross photosynthetic productivities of the investigated biofilms. After eCA inhibition, the efflux of carbon dioxide (CO2) from the biofilms increased two- to four-fold. This could be explained by the conversion of CO2, leaking from cyanobacterial cells, by eCA, to bicarbonate. Bicarbonate is then taken up again by the cyanobacteria. In suspensions, eCA reduced the CO2 leakage to the bulk medium from 90 to 50%. In biofilms cultivated at low bicarbonate concentration (~0.13 mM), the oxygen production was reduced by a similar ratio upon eCA inhibition. The role of eCA in intact biofilms was much less significant compared to biomass suspensions, as CO2 loss to the medium is reduced due to mass transfer resistance.

Microbial diversity associated with the anaerobic sediments of a soda lake (Mono Lake, California, USA)

Soda lakes are inhabited by important haloalkaliphilic microbial communities that are well adapted to these extreme characteristics. The surface waters of the haloalkaline Mono Lake (California, USA) are alkaline but, in contrast to its bottom waters, do not present high salinity. We have studied the microbiota present in the shoreline sediments of Mono Lake using next-generation sequencing techniques. The statistical indexes showed that Bacteria had a higher richness, diversity, and evenness than Archaea. Seventeen phyla and 8 “candidate divisions” were identified among the Bacteria, with a predominance of the phyla Firmicutes, Proteobacteria, and Bacteroidetes. Among the Proteobacteria, there was a notable presence of Rhodoplanes and a high diversity of sulfate-reducing Deltaproteobacteria, in accordance with the high sulfate-reducing activity detected in soda lakes. Numerous families of bacterial fermenters were identified among the Firmicutes. The Bacteroides were represented by several environmental groups that have not yet been isolated. Since final organic matter in anaerobic environments with high sulfate contents is mineralized mainly by sulfate-reducing bacteria, very little methanogenic archaeal biodiversity was detected. Only 2 genera, Methanocalculus and Methanosarcina, were retrieved. The species similarities described indicate that a significant number of the operational taxonomic units identified may represent new species.

Contrasting the Genetic Patterns of Microbial Communities in Soda Lakes with and without Cyanobacterial Bloom

Soda lakes have high levels of sodium carbonates and are characterized by salinity and elevated pH. These ecosystems are found across Africa, Europe, Asia, Australia, North, Central, and South America. Particularly in Brazil, the Pantanal region has a series of hundreds of shallow soda lakes (ca. 600) potentially colonized by a diverse haloalkaliphilic microbial community. Biological information of these systems is still elusive, in particular data on the description of the main taxa involved in the biogeochemical cycling of life-important elements. Here, we used metagenomic sequencing to contrast the composition and functional patterns of the microbial communities of two distinct soda lakes from the sub-region Nhecolândia, state of Mato Grosso do Sul, Brazil. These two lakes differ by permanent cyanobacterial blooms (Salina Verde, green-water lake) and by no record of cyanobacterial blooms (Salina Preta, black-water lake). The dominant bacterial species in the Salina Verde bloom was Anabaenopsis elenkinii. This cyanobacterium altered local abiotic parameters such as pH, turbidity, and dissolved oxygen and consequently the overall structure of the microbial community. In Salina Preta, the microbial community had a more structured taxonomic profile. Therefore, the distribution of metabolic functions in Salina Preta community encompassed a large number of taxa, whereas, in Salina Verde, the functional potential was restrained across a specific set of taxa. Distinct signatures in the abundance of genes associated with the cycling of carbon, nitrogen, and sulfur were found. Interestingly, genes linked to arsenic resistance metabolism were present at higher abundance in Salina Verde and they were associated with the cyanobacterial bloom. Collectively, this study advances fundamental knowledge on the composition and genetic potential of microbial communities inhabiting tropical soda lakes.

Nesterenkonia cremea sp. nov., a bacterium isolated from a soda lake

A Gram-stain-positive, aerobic, non-motile, rod-shaped, non-endospore-forming bacterial strain, 10CT, was isolated from Lonar soda lake in India. Based on the 16S rRNA gene sequence analysis, this strain was identified as belonging to the genus Nesterenkonia and was most closely related to the type strains of Nesterenkonia lacusekhoensis (99.1 %, sequence similarity), Nesterenkonia aethiopica (96.9 %), Nesterenkonia flava (96.9 %) and related of the genus Nesterenkonia (<96.6 %, sequence similarity). However, the DNA-DNA relatedness of strain 10CT with N. lacusekhoensis KCTC 19283T was only 34.6±0.9. The DNA G+C content of strain 10CT was 68.6 mol%. Strain 10CT was an aerobic microbe with optimal growth at 37 °C, pH 7.5-8.0 and 5-6 % (w/v) NaCl. The cell-wall peptidoglycan of strain 10CT was of the type A4α (l-Lys-l-Glu). The major polar lipids present were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. The major isoprenoid quinones were MK-7, MK-8 and MK-9. Major fatty acids of strain 10CT were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The results of phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strain 10CT, which represents a novel member of the genus Nesterenkonia for which the name Nesterenkonia cremea sp. nov. is proposed. The type strain is 10CT (=LMG 29100T=KCTC 39636T=CGMCC 1.15388T).

Emended description of the family Chromatiaceae, phylogenetic analyses of the genera Alishewanella, Rheinheimera and Arsukibacterium, transfer of Rheinheimera longhuensis LH2-2T to the genus Alishewanella and description of Alishewanella alkalitolerans sp. nov. from Lonar Lake, India

Phylogenetic analyses were performed for members of the family Chromatiaceae, signature nucleotides deduced and the genus Alishewanella transferred to Chromatiaceae. Phylogenetic analyses were executed for the genera Alishewanella, Arsukibacterium and Rheinheimera and the genus Rheinheimera is proposed to be split, with the creation of the Pararheinheimera gen. nov. Furthermore, the species Rheinheimera longhuensis, is transferred to the genus Alishewanella as Alishewanella longhuensis comb. nov. Besides, the genera Alishewanella and Rheinheimera are also emended. Strain LNK-7.1^T was isolated from a water sample from the Lonar Lake, India. Cells were Gram-negative, motile rods, positive for catalase, oxidase, phosphatase, contained C_16:0, C_17:1ω8c, summed feature3 (C_16:1ω6c and/or C_16:1ω7c) and summed feature 8 (C_18:1ω7c) as major fatty acids, PE and PG as the major lipids and Q-8 as the sole respiratory quinone. Phylogenetic analyses using NJ, ME, ML and Maximum parsimony, based on 16S rRNA gene sequences, identified Alishewanella tabrizica RCRI4^T as the closely related species of strain LNK-7.1^T with a 16S rRNA gene sequence similarity of 98.13%. The DNA-DNA similarity between LNK-7.1^T and the closely related species (A. tabrizica) was only 12.0% and, therefore, strain LNK-7.1^T was identified as a novel species of the genus Alishewanella with the proposed name Alishewanella alkalitolerans sp. nov. In addition phenotypic characteristics confirmed the species status to strain LNK-7.1^T. The type strain of A. alkalitolerans is LNK-7.1^T (LMG 29592^T = KCTC 52279^T), isolated from a water sample collected from the Lonar lake, India.

Soda pans of the Pannonian steppe harbor unique bacterial communities adapted to multiple extreme conditions

Soda pans of the Pannonian steppe are unique environments regarding their physical and chemical characteristics: shallowness, high turbidity, intermittent character, alkaline pH, polyhumic organic carbon concentration, hypertrophic condition, moderately high salinity, sodium and carbonate ion dominance. The pans are highly productive environments with picophytoplankton predominance. Little is known about the planktonic bacterial communities inhabiting these aquatic habitats; therefore, amplicon sequencing and shotgun metagenomics were applied to reveal their composition and functional properties. Results showed a taxonomically complex bacterial community which was distinct from other soda lakes regarding its composition, e.g. the dominance of class Alphaproteobacteria was observed within phylum Proteobacteria. The shotgun metagenomic analysis revealed several functional gene components related to the harsh and at the same time hypertrophic environmental conditions, e.g. proteins involved in stress response, transport and hydrolase systems targeting phytoplankton-derived organic matter. This is the first detailed report on the indigenous planktonic bacterial communities coping with the multiple extreme conditions present in the unique soda pans of the Pannonian steppe.

Microbial communities associated with the anthropogenic, highly alkaline environment of a saline soda lime, Poland

Soda lime is a by-product of the Solvay soda process for the production of sodium carbonate from limestone and sodium chloride. Due to a high salt concentration and alkaline pH, the lime is considered as a potential habitat of haloalkaliphilic and haloalkalitolerant microbial communities. This artificial and unique environment is nutrient-poor and devoid of vegetation, due in part to semi-arid, saline and alkaline conditions. Samples taken from the surface layer of the lime and from the depth of 2 m (both having pH ~11 and EC_e up to 423 dS m⁻¹) were investigated using culture-based (culturing on alkaline medium) and culture-independent microbiological approaches (microscopic analyses and pyrosequencing). A surprisingly diverse bacterial community was discovered in this highly saline, alkaline and nutrient-poor environment, with the bacterial phyla Proteobacteria (representing 52.8% of the total bacterial community) and Firmicutes (16.6%) showing dominance. Compared to the surface layer, higher bacterial abundance and diversity values were detected in the deep zone, where more stable environmental conditions may occur. The surface layer was dominated by members of the genera Phenylobacterium, Chelativorans and Skermanella, while in the interior layer the genus Fictibacillus was dominant. The culturable aerobic, haloalkaliphilic bacteria strains isolated in this study belonged mostly to the genus Bacillus and were closely related to the species Bacillus pseudofirmus, B. cereus, B. plakortidis, B. thuringensis and B. pumilus.

Salinity Affects the Composition of the Aerobic Methanotroph Community in Alkaline Lake Sediments from the Tibetan Plateau

Lakes are widely distributed on the Tibetan Plateau, which plays an important role in natural methane emission. Aerobic methanotrophs in lake sediments reduce the amount of methane released into the atmosphere. However, no study to date has analyzed the methanotroph community composition and their driving factors in sediments of these high-altitude lakes (>4000 m). To provide new insights on this aspect, the abundance and composition in the sediments of six high-altitude alkaline lakes (including both freshwater and saline lakes) on the Tibetan Plateau were studied. The quantitative PCR, terminal restriction fragment length polymorphism, and 454-pyrosequencing methods were used to target the pmoA genes. The pmoA gene copies ranged 10⁴-10⁶ per gram fresh sediment. Type I methanotrophs predominated in Tibetan lake sediments, with Methylobacter and uncultivated type Ib methanotrophs being dominant in freshwater lakes and Methylomicrobium in saline lakes. Combining the pmoA-pyrosequencing data from Tibetan lakes with other published pmoA-sequencing data from lake sediments of other regions, a significant salinity and alkalinity effect (P = 0.001) was detected, especially salinity, which explained ∼25% of methanotroph community variability. The main effect was Methylomicrobium being dominant (up to 100%) in saline lakes only. In freshwater lakes, however, methanotroph composition was relatively diverse, including Methylobacter, Methylocystis, and uncultured type Ib clusters. This study provides the first methanotroph data for high-altitude lake sediments (>4000 m) and shows that salinity is a driving factor for the community composition of aerobic methanotrophs.