Study of Bacterial Community Composition and Correlation of Environmental Variables in Rambla Salada, a Hypersaline Environment in South-Eastern Spain

Microbial diversity in polyextreme salt flats and their potential applications

Recent geological, hydrochemical, and mineralogical studies performed on hypersaline salt flats have given insights into similar geo-morphologic features on Mars. These salt-encrusted depressions are widely spread across the Earth, where they are characterized by high salt concentrations, intense UV radiation, high evaporation, and low precipitation. Their surfaces are completely dry in summer; intermittent flooding occurs in winter turning them into transitory hypersaline lakes. Thanks to new approaches such as culture-dependent, culture-independent, and metagenomic-based methods, it is important to study microbial life under polyextreme conditions and understand what lives in these dynamic ecosystems and how they function. Regarding these particular features, new halophilic microorganisms have been isolated from some salt flats and identified as excellent producers of primary and secondary metabolites and granules such as halocins, enzymes, carotenoids, polyhydroxyalkanoates, and exopolysaccharides. Additionally, halophilic microorganisms are implemented in heavy metal bioremediation and hypersaline wastewater treatment. As a result, there is a growing interest in the distribution of halophilic microorganisms around the world that can be looked upon as good models to develop sustainable biotechnological processes for all fields. This review provides insights into diversity, ecology, metabolism, and genomics of halophiles in hypersaline salt flats worldwide as well as their potential uses in biotechnology.

Metagenomics-Based Microbial Ecological Community Threshold and Indicators of Anthropogenic Disturbances in Estuarine Sediments

Assessing the impacts of cumulative anthropogenic disturbances on estuarine ecosystem health is challenging. Using spatially distributed sediments from the Pearl River Estuary (PRE) in southern China, which are significantly influenced by anthropogenic activities, we demonstrated that metagenomics-based surveillance of benthic microbial communities is a robust approach to assess anthropogenic impacts on estuarine benthic ecosystems. Correlational and threshold analyses between microbial compositions and environmental conditions indicated that anthropogenic disturbances in the PRE sediments drove the taxonomic and functional variations in the benthic microbial communities. An ecological community threshold of anthropogenic disturbances was identified, which delineated the PRE sediments into two groups (H and L) with distinct taxa and functional traits. Group H, located nearshore and subjected to a higher level of anthropogenic disturbances, was enriched with pollutant degraders, putative human pathogens, fecal pollution indicators, and functional traits related to stress tolerance. In contrast, Group L, located offshore and subjected to a lower level of anthropogenic disturbances, was enriched with halotolerant and oligotrophic taxa and functional traits related to growth and resource acquisition. The machine learning random forest model identified a number of taxonomic and functional indicators that could differentiate PRE sediments between Groups H and L. The identified ecological community threshold and microbial indicators highlight the utility of metagenomics-based microbial surveillance in assessing the adverse impacts of anthropogenic disturbances in estuarine sediments, which can assist environmental management to better protect ecosystem health.

Bioprospecting of unexplored halophilic actinobacteria against human infectious pathogens

Human pathogenic diseases received much attention recently due to their uncontrolled spread of antimicrobial resistance (AMR) which causes several threads every year. Effective alternate antimicrobials are urgently required to combat those disease causing infectious microbes. Halophilic actinobacteria revealed huge potentials and unexplored cultivable/non-cultivable actinobacterial species producing enormous antimicrobials have been proved in several genomics approaches. Potential gene clusters, PKS and NRPKS from Nocardia, Salinospora, Rhodococcus, and Streptomyces have wide range coding genes of secondary metabolites. Biosynthetic pathways identification via various approaches like genome mining, In silico, OSMAC (one strain many compound) analysis provides better identification of knowing the active metabolites using several databases like AMP, APD and CRAMPR, etc. Genome constellations of actinobacteria particularly the prediction of BGCs (Biosynthetic Gene Clusters) to mine the bioactive molecules such as pigments, biosurfactants and few enzymes have been reported for antimicrobial activity. Saltpan, saltlake, lagoon and haloalkali environment exploring potential actinobacterial strains Micromonospora, Kocuria, Pseudonocardia, and Nocardiopsis revealed several acids and ester derivatives with antimicrobial potential. Marine sediments and marine macro organisms have been found as significant population holders of potential actinobacterial strains. Deadly infectious diseases (IDs) including tuberculosis, ventilator-associated pneumonia and Candidiasis, have been targeted by halo-actinobacterial metabolites with promising results. Methicillin resistant Staphylococus aureus and virus like Encephalitic alphaviruses were potentially targeted by halophilic actinobacterial metabolites by the compound Homoseongomycin from sponge associated antinobacterium. In this review, we discuss the potential antimicrobial properties of various biomolecules extracted from the unexplored halophilic actinobacterial strains specifically against human infectious pathogens along with prospective genomic constellations.

Metagenomic Analysis Reveals the Response of Microbial Communities and Their Functions in Lake Sediment to Environmental Factors

Jingpo Lake is the largest mountain barrier lake in China and plays a key role in breeding, power generation, and providing a source of drinking water. Microbes are important participants in the formation of lake resources and energy cycles. However, the ecological protection of Jingpo Lake has faced serious challenges in recent years. In this study, we investigate the responses of the microbial community's composition of sediments at five locations to an environmental gradient representing water quality and water-depth changes using a metagenomic sequence. We found that the diversity and composition of the microbiota sediments were altered spatially and correlated with the physicochemical factors of water samples. In the microbial community, relatively lower Chao1, alternating conditional expectations, and Shannon and Simpson indices were found at the shallowest location with higher total phosphorus and chlorophyll a. Furthermore, the Kyoto Encyclopedia of Genes and Genomes analysis revealed that the metabolism function was the most abundant functional classification in Jingpo Lake. The levels of total phosphorus, chlorophyll a and pH were positively correlated with the abundance of Flavobacterium and the bacterial functions of the carbohydrate metabolism and amino acid metabolism. In conclusion, our results reveal the physical and chemical characteristics, as well as the microbial community characteristics, of Jingpo Lake, which provides new insights for studying the relationship between environmental factors and the bacterial community distribution of freshwater ecosystems, in addition to also providing a theoretical basis for the environmental monitoring and protection of the lake.

Hanstruepera marina sp. nov. and Hanstruepera flava sp. nov., two novel species in the family Flavobacteriaceae isolated by a modified in situ cultivation technique from marine sediment

A modified in situ cultivation technique was developed and applied to resource mining of uncultured microbes from marine sediments of Meishan Island in the East China Sea. Two novel strains NBU2968T and NBU2984T were isolated by this method but not standard Petri dish, which indicated the modified technique was more effective compared to conventional approaches for isolating uncultured microbes and could be popularized and applied to other aquatic environments. The two novel strains were identified by the polyphasic taxonomic approach. Cells of both strains were observed to be Gram-staining-negative, rod-shaped, nonmotile, aerobic, and yellow-pigmented. Catalase and oxidase activities and hydrolysis of Tweens 40, 60, and 80 of two novel strains were positive. Methyl red reaction, H2S production, and hydrolysis of Tween 20 were negative. According to 16S rRNA gene sequence analysis, two novel strains shared the highest similarities (96.4-97.7%) to the species with a validated name in the genus Hanstruepera, while shared lower sequence similarities (<95.6%) to all other genera. Phylogenetic analysis revealed that strains NBU2968T and NBU2984T were affiliated with the genus Hanstruepera. ANI and dDDH values between the two novel strains and Hanstruepera species were 77.4-78.3% and 20.4-20.9%, respectively, which were below the thresholds for species delineation. The 16S rRNA gene sequence similarity, ANI, and dDDH values between the two novel strains were 99.3, 88.9, and 36.3%, respectively, indicating that the two strains represent different species. The genomes of NBU2968T and NBU2984T were 3.28 Mbp with a G+C content of 34.2% and 3.09 Mbp with a G+C content of 34.4%, respectively. The only respiratory quinone was menaquinone-6 (MK-6). The major cellular fatty acids were iso-C15:0, iso-C15:1G, and iso-C17:0 3-OH. The major polar lipids of the two strains were phosphatidylethanolamine, unidentified amino lipids, and unidentified lipids. Based on the above polyphasic characteristics, strains NBU2968T and NBU2984T represent two novel species within the genus Hanstruepera, for which the names Hanstruepera marina sp. nov. and Hanstruepera flava sp. nov. are proposed. The type strains are NBU2968T (= MCCC 1K06392T= KCTC 82913T) and NBU2984T (= MCCC 1K07472T= KCTC 92511T), respectively.

Does a decrease in microbial biomass alter mycorrhizal attributes and soil quality indicators in coal mining areas under revegetation process?

Losses of microbial diversity in degraded ecosystems still have obscure consequences, especially when considering the interaction between arbuscular mycorrhizal fungi (AMF) and soil bacteria. This study investigates the effect of decreasing microbial biomass on mycorrhizal attributes and soil quality indicators. The dilution-to-extinction approach was applied in microcosms to search for associations among bacterial diversity, mycorrhizal attributes, and soil quality indicators. The experiment was conducted with four soil treatments (undiluted control 10⁰ = D0, 10^-3 = D3, 10^-6 = D6, and 10^-9 = D9) from a short-term (two years = 2Y) and a long-term (15 years = 15Y) coal mine revegetation area. Microcosms were inoculated with 300 spores of Acaulospora colombiana, Gigaspora albida, and Claroideoglomus etunicatum with millet as the host plant. Results included the total number of AMF spores, mycorrhizal colonization, soil aggregation, glomalin, fluorescein diacetate hydrolysis (FDA), basal soil respiration, microbial biomass, and soil bacterial microbiome. Larger differences were observed between areas than between dilution treatments within the sampling area. Attributes that presented differences in the dilutions compared to D0 2Y samples were mycorrhizal colonization (D0 = 85% and D9 = 43.3%), FDA (D0 = 77.2% and D9 = 55.5%), extractable glomalin-related soil protein (D0 = 0.09 and D9 = 0.11) and bacterial diversity (D0 = 7.3 and D6 = 5.3). D0 15Y samples presented differences in microbial biomass nitrogen (D0: 232.0) and bacterial diversity (D0: 7.9, D9: 5.6) compared to the dilutions. Bacterial microbiome present in the D0 samples formed distinct clusters as to other samples and correlated with soil aggregation and basal respiration attributes. Results suggest that AMF inoculation and dilution-to-extinction did not affect soil quality indicators preeminently, but the bacterial community is affected and can influence the process of environmental revegetation. A long-term revegetation period is substantial to improve quality indicators and establish the diversity of microorganisms and consequently revegetation in areas impacted by coal mining.

Evaluation of antimicrobial and antiproliferative activities of Actinobacteria isolated from the saline lagoons of northwestern Peru

Extreme environments Morrope and Bayovar Salt lagoons, several ecosystems and microhabitats remain unexplored, and little is known about the diversity of Actinobacteria. We suggest that the endemic bacteria present in this extreme environment is a source of active molecules with anticancer, antimicrobial, and antiparasitic properties. Using phenotypic and genotypic characterization techniques, including 16S rRNA sequencing, we identified these bacteria as members of the genera Streptomyces, Pseudonocardia, Staphylococcus, Bacillus, and Pseudomonas. Actinobacteria strains were found predominantly. Phylogenetic analysis revealed 13 Actinobacteria clusters of Streptomyces, the main genus. Three Streptomycetes, strains MW562814, MW562805, and MW562807 showed antiproliferative activities against three tumor cell lines: U251 glioma, MCF7 breast, and NCI-H460 lung (non-small cell type); and antibacterial activity against Staphylococcus aureus ATCC 6538, Escherichia coli ATCC 10536, and the multidrug resistant Acinetobacter baumannii AC-972. The antiproliferative activities (measured as total growth inhibition [TGI]) of Streptomyces sp. MW562807 were 0.57 μg/mL, for 0.61 μg/mL, and 0.80 μg/mL for glioma, lung non-small cell type, and breast cancer cell lines, respectively; the methanolic fraction of the crude extract showed a better antiproliferative activity and could inhibit the growth of (U251 (TGI = 38.3 μg/mL), OVCAR-03 (TGI = 62.1 μg/mL), and K562 (TGI = 81.5 μg/mL)) of nine tumor cells types and one nontumor cell type. Extreme enviroments, such as the Morrope and Bayovar Salt saloons are promising sources of new bacteria, whose compounds may be useful for treating various infectious diseases or even some types of cancer.

Taxogenomic and Metabolic Insights into Marinobacterium ramblicola sp. nov., a New Slightly Halophilic Bacterium Isolated from Rambla Salada, Murcia

A Gram-negative, motile, rod-shaped bacteria, designated D7^T, was isolated by using the dilution-to-extinction method, from a soil sample taken from Rambla Salada (Murcia, Spain). Growth of strain D7^T was observed at 15–40 °C (optimum, 37 °C), pH 5–9 (optimum, 7) and 0–7.5% (w/v) NaCl (optimum, 3%). It is facultatively anaerobic. Phylogenetic analysis based on 16S rRNA gene sequence showed it belongs to the genus Marinobacterium. The in silico DDH and ANI against closest Marinobacterium relatives support its placement as a new species within this genus. The major fatty acids of strain D7^T were C_16:0, summed feature 3 (C_16:1 ω7c/C_16:1 ω6c) and summed feature 8 (C_18:1 ω7c/C_18:1 ω6c). The polar lipid profile consists of phosphatidylethanolamine, phosphatidylglycerol and two uncharacterized lipids. Ubiquinone 8 was the unique isoprenoid quinone detected. The DNA G + C content was 59.2 mol%. On the basis of the phylogenetic, phenotypic, chemotaxonomic and genomic characterization, strain D7^T (= CECT 9818^T = LMG 31312^T) represents a novel species of the genus Marinobacterium for which the name Marinobacterium ramblicola sp. nov. is proposed. Genome-based metabolic reconstructions of strain D7^T suggested a heterotrophic and chemolitotrophic lifestyle, as well as the capacity to biosynthetize and catabolize compatible solutes, and to degrade hydrocarbon aromatic compounds.

Ubiquitousness of Haloferax and Carotenoid Producing Genes in Arabian Sea Coastal Biosystems of India

This study presents a comparative analysis of halophiles from the global open sea and coastal biosystems through shotgun metagenomes (n = 209) retrieved from public repositories. The open sea was significantly enriched with Prochlorococcus and Candidatus pelagibacter. Meanwhile, coastal biosystems were dominated by Marinobacter and Alcanivorax. Halophilic archaea Haloarcula and Haloquandratum, predominant in the coastal biosystem, were significantly (p < 0.05) enriched in coastal biosystems compared to the open sea. Analysis of whole genomes (n = 23,540), retrieved from EzBioCloud, detected crtI in 64.66% of genomes, while cruF was observed in 1.69% Bacteria and 40.75% Archaea. We further confirmed the viability and carotenoid pigment production by pure culture isolation (n = 1351) of extreme halophiles from sediments (n = 410 × 3) sampling at the Arabian coastline of India. All red-pigmented isolates were represented exclusively by Haloferax, resistant to saturated NaCl (6 M), and had >60% G + C content. Multidrug resistance to tetracycline, gentamicin, ampicillin, and chloramphenicol were also observed. Our study showed that coastal biosystems could be more suited for bioprospection of halophiles rather than the open sea.

Raiders of the Lost Correlation: A Guide on Using Pearson and Spearman Coefficients to Detect Hidden Correlations in Medical Sciences

Pearson and Spearman correlations are important tools for all scientific fields and are widely used in medical sciences, especially during the current COVID-19 pandemic emergency. This technical report has shown that conventional criteria for evaluating the adoption of these coefficients can conceal substantial scientific information regarding correlations that occur above or below a certain threshold. In particular, the Pearson coefficient can reveal hidden correlations even when data are not normally distributed. Finally, an optimized operational guide to reveal any hidden correlation is reported.

Transient Dynamics of Archaea and Bacteria in Sediments and Brine Across a Salinity Gradient in a Solar Saltern of Goa, India

The microbial fluctuations along an increasing salinity gradient during two different salt production phases – initial salt harvesting (ISH) phase and peak salt harvesting (PSH) phase of Siridao solar salterns in Goa, India were examined through high-throughput sequencing of 16S rRNA genes on Illumina MiSeq platform. Elemental analysis of the brine samples showed high concentration of sodium (Na⁺) and chloride (Cl^–) ions thereby indicating its thalassohaline nature. Comparison of relative abundance of sequences revealed that Archaea transited from sediment to brine while Bacteria transited from brine to sediment with increasing salinity. Frequency of Archaea was found to be significantly enriched even in low and moderate salinity sediments with their relative sequence abundance reaching as high as 85%. Euryarchaeota was found to be the dominant archaeal phylum containing 19 and 17 genera in sediments and brine, respectively. Phylotypes belonging to Halorubrum, Haloarcula, Halorhabdus, and Haloplanus were common in both sediments and brine. Occurence of Halobacterium and Natronomonas were exclusive to sediments while Halonotius was exclusive to brine. Among sediments, relative sequence frequency of Halorubrum, and Halorhabdus decreased while Haloarcula, Haloplanus, and Natronomonas increased with increasing salinity. Similarly, the relative abundance of Haloarcula and Halorubrum increased with increasing salinity in brine. Sediments and brine samples harbored about 20 and 17 bacterial phyla, respectively. Bacteroidetes, Proteobacteria, and Chloroflexi were the common bacterial phyla in both sediments and brine while Firmicutes were dominant albeit in sediments alone. Further, Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria were observed to be the abundant class within the Proteobacteria. Among the bacterial genera, phylotypes belonging to Rubricoccus and Halomonas were widely detected in both brine and sediment while Thioalkalispira, Desulfovermiculus, and Marinobacter were selectively present in sediments. This study suggests that Bacteria are more susceptible to salinity fluctuations than Archaea, with many bacterial genera being compartment and phase-specific. Our study further indicated that Archaea rather than Bacteria could withstand the wide salinity fluctuation and attain a stable community structure within a short time-frame.

Isolation and diversity of sediment bacteria in the hypersaline aiding lake, China

Halophiles are relatively unexplored as potential sources of novel species. However, little is known about the culturable bacterial diversity thrive in hypersaline lakes. In this work, a total of 343 bacteria from sediment samples of Aiding Lake, China, were isolated using nine different media supplemented with 5% or 15% (w/v) NaCl. The number of species and genera of bacteria recovered from the different media varied, indicating the need to optimize the isolation conditions. The results showed an unexpected level of bacterial diversity, with four phyla (Actinobacteria, Firmicutes, Proteobacteria, and Rhodothermaeota), fourteen orders (Actinopolysporales, Alteromonadales, Bacillales, Balneolales, Chromatiales, Glycomycetales, Jiangellales, Micrococcales, Micromonosporales, Oceanospirillales, Pseudonocardiales, Rhizobiales, Streptomycetales, and Streptosporangiales), including 17 families, 43 genera (including two novel genera), and 71 species (including four novel species). The predominant phyla included Actinobacteria and Firmicutes and the predominant genera included Actinopolyspora, Gracilibacillus, Halomonas, Nocardiopsis, and Streptomyces. To our knowledge, this is the first time that members of phylum Rhodothermaeota were identified in sediment samples from a salt lake.

Roseovarius bejariae sp. nov., a moderately halophilic bacterium isolated from a hypersaline steep-sided river bed

An aerobic, Gram-stain-negative ovoid, designated as strain A21T, was isolated using the dilution-to-extinction method from a soil sample taken from Rambla Salada, an athalassohaline habitat located in Murcia (south-eastern Spain). Strain A21T is non-motile, has a respiratory metabolism and grows at NaCl concentrations within the range 0.5–15 % (w/v) [optimum, 5 % (w/v)], at 5–35 °C (optimum, 28 °C) and at pH 6–8 (optimum, pH 7.0). This strain is positive for catalase activity, oxidase activity and nitrate reduction. The 16S rRNA gene sequence indicates that it belongs to the genus Roseovarius in the class Alphaproteobacteria . The most closely related species are Roseovarius pacificus and Roseovarius halotolerans to which the strain A21T shows 16S rRNA gene sequence similarity values of 98.06 and 97.7 %, respectively. The average nucleotide identity in blast and digital DNA–DNA hybridization values between strain A21T and R. pacificus LMG 24575T are 76.8 and 21 %, respectively. The DNA G+C content based on the genome is 61.28 mol%. The major fatty acids (>5 % of the total fatty acids) of strain A21T are C18 : 1 ω7c/C18 : 1 ω6c and C16 : 0. The only detected isoprenoid quinone in strain A21T is ubiquinone 10 (Q-10). The polar lipid profile contains phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and three unidentified polar lipids. Based on the phylogenetic, genotypic, phenotypic and chemotaxonomic data, the strain represents a novel species of the genus Roseovarius , for which the name Roseovarius bejariae sp. nov. is proposed. Strain A21T (=CECT 9817T=LMG 31311T) is the type strain.

Structuring biofilm communities living in pesticide contaminated water

The wide use of pesticides in agriculture expose microbiota to stressful conditions that require the development of survival strategies. The bacterial response to many pollutants has not been elucidated in detail, as well as the evolutionary processes that occur to build adapted communities. The purpose of this study was to evaluate the bacterial population structure and adaptation strategies in planktonic and biofilm communities in limited environments, as tanks containing water used for washing herbicide containers. This biodiversity, with high percentage of nonculturable microorganisms, was characterized based on habitat and abiotic parameters using molecular and bioinformatics tools. According to water and wastewater standards, the physicochemical conditions of the tank water were inadequate for survival of the identified bacteria, which had to develop survival strategies in this hostile environment. The biodiversity decreased in the transition from planktonic to biofilm samples, indicating a possible association between genetic drift and selection of individuals that survive under stressful conditions, such as heating in water and the presence of chlorine, fluorine and agrochemicals over a six-month period. The abundance of Enterobacter, Acinetobacter and Pseudomonas in biofilms from water tanks was linked to essential processes, deduced from the genes attributed to these taxonomic units, and related to biofilm formation, structure and membrane transport, quorum sensing and xenobiotic degradation. These characteristics were randomly combined and fixed in the biofilm community. Thus, communities of biofilm bacteria obtained under these environmental conditions serve as interesting models for studying herbicide biodegradation kinetics and the prospects of consortia suitable for use in bioremediation in reservoirs containing herbicide-contaminated wastewater, as biofilters containing biofilm communities capable of degrading herbicides.