Archaeal Phyla Research Articles

Microbial community diversity and composition in river sediments contaminated with tetrabromobisphenol A and copper

The microbial community composition in aquatic ecosystems have received increased attention. However, the knowledge gap relative to the responses of bacterial, archaeal and fungal communities in co-contaminated river sediments remain poorly studied. Here, we investigated the changes of tetrabromobisphenol A (TBBPA) and copper (Cu) concentrations and the responses of microbial communities in co-contaminated sediments during long-term incubation. TBBPA concentrations significantly decreased over time, whereas Cu concentrations remained relatively stable over the 60-day incubation. Abundances of the bacterial 16S rRNA, archaeal 16S rRNA and fungal ITS genes ranged from 6.53 × 106 to 1.26 × 109 copies g−1, 1.12 × 106 to 5.47 × 106 copies g−1 and 5.33 × 103 to 7.51 × 104 copies g−1 in the samples, respectively. A total of 11, 6 and 5 bacterial, archaeal and fungal phyla were identified across all samples. Bacterial, archaeal and fungal communities mainly consisted of members from the phyla Proteobacteria and Acidobacteria, Methanomicrobia and Woesearchaeia as well as Agaricales and Helotiales, respectively. Fungal communities showed a stronger response to pollutant addition after a long incubation compared with bacterial and archaeal communities. The variance analysis results revealed that the bacterial, archaeal and fungal microbial communities of all treatments were distinctly distributed into two separated clusters according to incubation time. However, the three microbial communities did not significantly change in response to pollutant types, which was consistent with variation in relative abundances of the three microbial communities. These findings improve our understanding of the ecotoxicological effects of co-exposure on sediment microbial communities.

Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika

Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth’s surface. LT’s mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT’s 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change, which is predicted to bring increased stratification and anoxia to freshwater lakes.

Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway

Asgard archaea are widely distributed in anaerobic environments. Previous studies revealed the potential capability of Asgard archaea to utilize various organic substrates including proteins, carbohydrates, fatty acids, amino acids and hydrocarbons, suggesting that Asgard archaea play an important role in sediment carbon cycling. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with the Asgard superphylum. The genomes of these archaea were recovered from metagenomes generated from mangrove sediments, and were found to encode alkyl/benzyl-succinate synthases and their activating enzymes that are similar to those identified in alkane-degrading sulfate-reducing bacteria. Hermodarchaeota also encode enzymes potentially involved in alkyl-coenzyme A and benzoyl-coenzyme A oxidation, the Wood–Ljungdahl pathway and nitrate reduction. These results indicate that members of this phylum have the potential to strictly anaerobically degrade alkanes and aromatic compounds, coupling the reduction of nitrate. By screening Sequence Read Archive, additional genes encoding 16S rRNA and alkyl/benzyl-succinate synthases analogous to those in Hermodarchaeota were identified in metagenomic datasets from a wide range of marine and freshwater sediments. These findings suggest that Asgard archaea capable of degrading alkanes and aromatics via formation of alkyl/benzyl-substituted succinates are ubiquitous in sediments.

Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea.

Ribosomes are intricate molecular machines ensuring proper protein synthesis in every cell. Ribosome biogenesis is a complex process which has been intensively analyzed in bacteria and eukaryotes. In contrast, our understanding of the in vivo archaeal ribosome biogenesis pathway remains less characterized. Here, we have analyzed the in vivo role of the almost universally conserved ribosomal RNA dimethyltransferase KsgA/Dim1 homolog in archaea. Our study reveals that KsgA/Dim1-dependent 16S rRNA dimethylation is dispensable for the cellular growth of phylogenetically distant archaea. However, proteomics and functional analyses suggest that archaeal KsgA/Dim1 and its rRNA modification activity (i) influence the expression of a subset of proteins and (ii) contribute to archaeal cellular fitness and adaptation. In addition, our study reveals an unexpected KsgA/Dim1-dependent variability of rRNA modifications within the archaeal phylum. Combining structure-based functional studies across evolutionary divergent organisms, we provide evidence on how rRNA structure sequence variability (re-)shapes the KsgA/Dim1-dependent rRNA modification status. Finally, our results suggest an uncoupling between the KsgA/Dim1-dependent rRNA modification completion and its release from the nascent small ribosomal subunit. Collectively, our study provides additional understandings into principles of molecular functional adaptation, and further evolutionary and mechanistic insights into an almost universally conserved step of ribosome synthesis.

Organic carbon and microbiome in tundra and forest–tundra permafrost soils, southern Yamal, Russia

Permafrost soils differ significantly from other soils because they serve as a huge reservoir for organic carbon accumulated during the Quaternary Period, which is at risk of being released as the Arctic warms. This study aimed to characterize existing carbon pools, delineate possible mineralization risks of soil organic matter and assess microbial communities in the tundra and forest–tundra permafrost soils of the southern Yamal region of Russia. The profile distribution of carbon, nitrogen and the C:N ratio showed non-gradual changes with depth due to the manifestation of cryopedogenesis in soil profiles, which lead to cryogenic mass transfer. Mean carbon stocks for the study area were 7.85 ± 2.24 kg m−2 (0–10 cm layer), 14.97 ± 5.53 kg m−2 (0–30 cm) and 23.99 ± 8.00 kg m−2 (0–100 cm). The analysis of the humus type revealed a predominance of fulvic type and low-molecular-weight fragments in the fulvic acid fraction, which indicates high mineralization risk of humic substances under Arctic warming conditions. The taxonomic analysis of soil microbiomes revealed 48 bacterial and archaeal phyla, among which proteobacteria (27%) and actinobacteria (20%) were predominant. The pH range and nitrogen accumulation were the main environmental determinants of microbial community diversity and composition in the studied soils.

Characterization of Metagenome-Assembled Genomes and Carbohydrate-Degrading Genes in the Gut Microbiota of Tibetan Pig.

Tibetan pig is an important domestic mammal, providing products of high nutritional value for millions of people living in the Qinghai-Tibet Plateau. The genomes of mammalian gut microbiota encode a large number of carbohydrate-active enzymes, which are essential for the digestion of complex polysaccharides through fermentation. However, the current understanding of microbial degradation of dietary carbohydrates in the Tibetan pig gut is limited. In this study, we produced approximately 145 gigabases of metagenomic sequence data for the fecal samples from 11 Tibetan pigs. De novo assembly and binning recovered 322 metagenome-assembled genomes taxonomically assigned to 11 bacterial phyla and two archaeal phyla. Of these genomes, 191 represented the uncultivated microbes derived from novel prokaryotic taxa. Twenty-three genomes were identified as metagenomic biomarkers that were significantly abundant in the gut ecosystem of Tibetan pigs compared to the other low-altitude relatives. Further, over 13,000 carbohydrate-degrading genes were identified, and these genes were more abundant in some of the genomes within the five principal phyla: Firmicutes, Bacteroidetes, Spirochaetota, Verrucomicrobiota, and Fibrobacterota. Particularly, three genomes representing the uncultivated Verrucomicrobiota encode the most abundant degradative enzymes in the fecal microbiota of Tibetan pigs. These findings should substantially increase the phylogenetic diversity of specific taxonomic clades in the microbial tree of life and provide an expanded repertoire of biomass-degrading genes for future application to microbial production of industrial enzymes.

The microbial community structure of the Dupnisa cave in Kırklareli, Turkey

Cave ecosystems count to be extreme environments due to their stable temperature, darkness, high humidity rates, and limited organic materials. In this context, these ecosystems represent invaluable laboratories for microbiological studies. Although there are common features between the microorganism groups obtained from the culture-based microbiological studies conducted in the caves and the groups highlighted through molecular methods, the microorganism groups determined through this last method are richer. The detected microorganisms are variable depending on the characteristics of each cave. The aim of this study is to determine the microbial diversity in samples taken from 5 different regions (including regions visited by tourists) of Dupnisa Cave and to reveal the differences between these regions. This is the first microbiological study running in cave sediments of Dupnisa Cave System situated in the north-western of Turkey. In this study, using the Illumina MiSeq next-generation sequencing approach for analyses of Dupnisa Cave samples, 14 phyla and 298 genera as well as 2 phyla and 20 genera can be attributed to bacterial and archaea OTUs, respectively. Moreover, the bacterial community is dominated by the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Firmicutes, Nitrospirae, Chloroflexi and Acidobacteria distributed with 1 % and above. Archaeal community is represented by Thaumarchaeota and Euryarchaeota phyla. Proteobacteria is the most dominant bacterial phylum and Thaumarchaeota dominates the archaeal phyla. The highest number of types of bacteria according to Chao 1 richness estimation index were found at point AF (cave entrance / sediment), and that of types of archaea were found at point F2 (touristic area 2 / cave sediment). F2 was determined as the sampling point with the highest diversity of archaeal and bacterial genera according to Shannon-Wiener diversity index.

Methanogen Abundance Thresholds Capable of Differentiating In Vitro Methane Production in Human Stool Samples.

Intestinal methane (CH4) gas production has been associated with a number of clinical conditions and may have important metabolic and physiological effects. In this study, taxonomic and functional gene analyses and in vitro CH4 gas measurements were used to determine if molecular markers can potentially serve as clinical tests for colonic CH4 production. We performed a cross-sectional study involving full stool samples collected from 33 healthy individuals. In vitro CH4 gas measurements were obtained after 2-h incubation of stool samples and used to characterize samples as CH4 positive (CH4+) and CH4 negative (CH4-; n = 10 and 23, respectively). Next, we characterized the fecal microbiota through high-throughput DNA sequencing with a particular emphasis on archaeal phylum Euryarchaeota. Finally, qPCR analyses, targeting the mcrA gene, were done to determine the ability to differentiate CH4+ versus CH4- samples and to delineate major methanogen species associated with CH4 production. Methanobrevibacter was found to be the most abundant methane producer and its relative abundance provides a clear distinction between CH4+ versus CH4- samples. Its sequencing-based relative abundance detection threshold for CH4 production was calculated to be 0.097%. The qPCR-based detection threshold separating CH4+ versus CH4- samples, based on mcrA gene copies, was 5.2 × 105 copies/g. Given the decreased time-burden placed on patients, a qPCR-based test on a fecal sample can become a valuable tool in clinical assessment of CH4 producing status.

Taisui TS-2007S, a Large Microbial Mat Discovered in Soil in China.

In this study, Taisui TS-2007S, a previously unidentified biological object discovered in soil in China, was identified. TS-2007S was shown to contain abundant carbohydrates but a scarcity of protein, fat, and minerals. The exopolymers of TS-2007S showed FT-IR spectra that were similar to those of xanthan gum (XG) but that were dissimilar to those of polyvinyl alcohol (PVA). The NMR spectra of TS-2007S exopolymers in D2O were similar to those of PVA but differed from those of xanthan gum. Unlike PVA, TS-2007S exopolymers and xanthan gum were not soluble in dimethyl sulfoxide (DMSO). Furthermore, the exopolymers contained many monosaccharide components, including fucose, rhamnose, mannose, and glucuronic acid in a molar ratio of 87.90:7.49:4.45:0.15. The exopolymers also included traces of glucuronic acid, galactose, and xylose. Taken together, these results suggest that the exopolymers are microbial extracellular polymeric substances (EPSs). The microbial community structure in TS-2007S showed that the predominant bacterial, archaeal, and fungal phyla were Proteobacteria, Euryarchaeota, and Ascomycota at high relative abundances of 90.77, 97.15, and 87.43%, respectively, different from those observed in water and soil environments. Based on these results, we strongly propose that TS-2007S should be defined as a microbial mat formed in soil.

Prokaryotic Communities in Saline Soils of the Lake Elton Area in a Soil Catena along the Khara River

Analysis of the taxonomic structure of prokaryotic microbial complexes of the saline soils in the Lake Elton area and their comparative characteristics were carried out for a soil catena along the Khara River flowing into the hypersaline Lake Elton. High-throughput pyrosequencing detected 11 bacterial and 2 archaeal phyla. Comparative analysis of community structure revealed the differences between Solonchaks located at the river flood land and Kastanozems at the slope and top of the river terrace. The patterns of occurrence were described for six predominant phyla (Euryarchaeota, Thaumarchaeota, Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria). For the floodplain soils, the relations between the distribution of Euryarchaeota, Thaumarchaeota, Firmicutes, Actinobacteria, Proteobacteria and soil salinity as well as soil pH were described. Occurrence of members of the phyla Euryarchaeota, Thaumarchaeota, Firmicutes, Actinobacteria, and Proteobacteria in flood land soils was shown to depend on the soil salinity and pH. Members of the phyla Actinobacteria and Firmicutes were shown to predominate in Gleyic Kastanozems . Cloning of the 16S rRNA gene revealed high diversity within the genus Streptomyces (Actinobacteria). A number of the isolated streptomycete clones were homologous to the known antibiotic producers, which indicates that soils of this area are promising for further biotechnological screening.

Elucidating the archaeal community and functional potential in two typical coastal wetlands with different stress patterns

Archaea play dominant roles in nutrient cycling, but the archaeal community and function in coastal wetlands with different stress patterns remain poorly understood. Here, two typical coastal wetlands of the Yellow River estuary, Zone A with only tidal erosion and Zone B with runoff and tidal invasion, were selected to explore the possible differences in archaeal community and function and evaluate the influential factors. Compared with Zone B, Zone A had higher levels of total nitrogen, available phosphorous (AP) and pH. Thaumarchaeota was the most abundant archaeal phylum, followed by Euryarchaeota in Zones A and B. Candidatus_Nitrosopelagicus (30.85% in Zone A, 36.04% in Zone B) and Candidatus_Nitrosopumilus (24.10% in Zone A, 39.01% in Zone B) were the dominant ammonia-oxidizing archaea in both zones, and Haloarcula and Haloferax were the dominant denitrifying halophilic archaea in Zone A. Organisms from methanogenic genera Methanobrevibacter, Methanocorpusculum and Methanosarcina were enriched in Zone A. Anaerobic methanotrophic Candidatus_Methanoperedens (ANME-2d) had relatively low abundance in Zones A and B. These archaea were the key factors in maintaining the carbon and nitrogen cycles in coastal wetlands. Moreover, nitrification was relatively active in Zone B, and denitrification and methanogenesis dominated in Zone A. Redundancy analysis revealed that AP, NH4+–N, pH, salinity and moisture played important roles in the determination of archaeal community composition at the genus level. Microbial community and PICRUSt analysis indicated that the archaeal communities changed significantly, but the functions were relatively stable for both zones. This finding suggests that environmental selection in similar habitats could lead to functional convergence. The relative gene abundances of nitrate reductase were relatively high, indicating that aside from denitrification, a large amount of nitrite as an electron acceptor was present to perform nitrite-driven anaerobic methane oxidation via reverse methanogenesis. The findings help in understanding the impacts of different stress patterns on archaeal community composition and functional potential in coastal wetlands.

Molecular Logic of Prokaryotic Surface Layer Structures.

Most prokaryotic cells are encased in a surface layer (S-layer) consisting of a paracrystalline array of repeating lattice-forming proteins. S-layer proteins populate a vast and diverse sequence space, performing disparate functions in prokaryotic cells, including cellular defense, cell-shape maintenance, and regulation of import and export of materials. This article highlights recent advances in the understanding of S-layer structure and assembly, made possible by rapidly evolving structural and cell biology methods. We underscore shared assembly principles revealed by recent work and discuss a common molecular framework that may be used to understand the structural organization of S-layer proteins across bacteria and archaea.

Progress in elucidating the origin of eukaryotes

Knowledge of the origin of eukaryotes is key to broadening our understanding of the eukaryotic genome and the relationship among internal structures within a eukaryotic cell. Since the discovery of archaea in 1977 and the proposal of three-domain tree of life by the American microbiologist Carl Woese, the intimate relationship in evolution between eukaryotes and archaea has been demonstrated by considerable experiments and analyses. From the beginning of the 21st century, with the development of phylogenetic methods and the discovery of new archaeal phyla more related to eukaryotes, increasing evidence has shown that Eukarya and Archaea should be merged into one domain, leading to a two-domain tree of life. Nowadays, the Asgard superphylum discovered via metagenomic analysis is regarded as the closest prokaryotes to eukaryotes. Nevertheless, several key questions are still under debate, such as what the ancestors of the eukaryotes were and when mitochondria emerged. Here, we review the current research progress regarding the changes of the tree of life and the detailed eukaryotic evolutionary mechanism. We show that the recent findings have greatly improved our knowledge on the origin of eukaryotes, which will pave the way for future studies.

EXPLORING THE METABOLICALLY ACTIVE RUMEN MICROBIOTA AND ITS FIBROLYTIC POTENTIAL IN CROSSBRED CATTLE FED ON FIBROUS DIET THROUGH METATRANSCRIPTOMICS

The rumen wharves conglomerate of symbiotic fibrolytic microflora with the potential to produce repertoire of carbohydrate-active enzymes to elicit the degradation of recalcitrant plant lignocellulosic complex into simpler forms that can be utilized by the host. A metatranscriptomics approach was adopted to explore the metabolically active microbiota and the transcripts involved in the deconstruction of lignocellulose in Indian crossbred cattle rumen. The experimental animals were fed with mixed diet for a period of twenty-one days and the total RNA was isolated from the rumen digesta using a modified total RNA extraction protocol. After mRNA enrichment, the cDNA libraries were subjected to sequencing under Illumina HiSeq platform and generated about 2.89 GB of raw sequences. The contig assembly was accomplished using two different tools and the redundant sequences were removed before further processing. A total of 133,930 orfs were predicted from the assembled contigs using MetaGeneMark tool and the taxonomic affiliation of orfs were achieved using MEGAN 6.0 Community Edition. A total of 17 bacterial, 5 eukaryotic and 1 archaeal phylum were identified from rumen metatranscriptomic dataset. Phylum Bacteroidetes were acknowledged as the most abundant and metabolically active rumen bacterial populations in cattle rumen with 36,414 orfs corresponding to it, followed by Firmicutes with 6,349 orfs. Further, MEGAN annotation of metatranscriptomic data at species level revealed that Prevotella brevis and Prevotella ruminicola as the most metabolically active bacterial populations representing 4,022 and 2,725 orfs each. The functional annotation of metatranscriptomic data using COG database revealed that a large number of transcripts (~16%) were corresponding to translation, ribosomal structure and biogenesis and carbohydrate transport and metabolism (15%). dbCAN annotation of rumen metatranscriptomic data identified and classified 5,267 transcripts belonging to 168 CAZyme families (GH-52%, GT-26%, CBM-14%, CE-6%, PL-2% and AA-0%). The microbial community analysis of the CAZyme encoding transcripts using M5NR database revealed that a significant proportion of CAZymes were contributed by genera Prevotella (37%) and Bacteroides (21%). The cattle rumen microbiome metatranscriptome analysis presented in this study facilitated the detection of large number of transcripts encoding diverse CAZymes that actively take part in the hydrolysis of plant lignocellulose complex that may be useful for improving livestock and biofuel generation.

Use of additives in composting informed by experience from agriculture: Effects of nitrogen fertilizer synergists on gaseous nitrogen emissions and corresponding genes (amoA and nirS)

The effects of two nitrogen fertilizer synergists (urease inhibitor, UI; nitrification inhibitor, NI) on NH3 and N2O emissions and the successions of the amoA and nirS genes during composting were assessed. Results showed that the UI and UI + NI treatments reduced NH3 emissions by 26.3% and 24.3%, respectively, and N2O emissions were reduced by 63.9% for UI + NI treatment but were not reduced by UI. The addition of UI and NI significantly reduced the abundance of the nirS gene during thermophilic stage, while significantly increased that of the amoA gene during maturation stage. Crenarchaeota was the principal nitrifying archaeal phylum and was significantly affected by pH. Proteobacteria was the main denitrifying bacterial phylum, whose relative abundance was higher for UI + NI treatment than the other treatments. PICRUSt analysis showed that the addition of UI and NI inhibited enzymatic activity related to N transformation during thermophilic stage while enriching enzymatic activity during maturation phase.

The conserved ribonuclease aCPSF1 triggers genome-wide transcription termination of Archaea via a 3'-end cleavage mode.

Transcription termination defines accurate transcript 3′-ends and ensures programmed transcriptomes, making it critical to life. However, transcription termination mechanisms remain largely unknown in Archaea. Here, we reported the physiological significance of the newly identified general transcription termination factor of Archaea, the ribonuclease aCPSF1, and elucidated its 3′-end cleavage triggered termination mechanism. The depletion of Mmp-aCPSF1 in Methanococcus maripaludis caused a genome-wide transcription termination defect and disordered transcriptome. Transcript-3′end-sequencing revealed that transcriptions primarily terminate downstream of a uridine-rich motif where Mmp-aCPSF1 performed an endoribonucleolytic cleavage, and the endoribonuclease activity was determined to be essential to the in vivo transcription termination. Co-immunoprecipitation and chromatin-immunoprecipitation detected interactions of Mmp-aCPSF1 with RNA polymerase and chromosome. Phylogenetic analysis revealed that the aCPSF1 orthologs are ubiquitously distributed among the archaeal phyla, and two aCPSF1 orthologs from Lokiarchaeota and Thaumarchaeota could replace Mmp-aCPSF1 to terminate transcription of M. maripaludis. Therefore, the aCPSF1 dependent termination mechanism could be widely employed in Archaea, including Lokiarchaeota belonging to Asgard Archaea, the postulated archaeal ancestor of Eukaryotes. Strikingly, aCPSF1-dependent archaeal transcription termination reported here exposes a similar 3′-cleavage mode as the eukaryotic RNA polymerase II termination, thus would shed lights on understanding the evolutionary linking between archaeal and eukaryotic termination machineries.

Discovery of an Abundance of Biosynthetic Gene Clusters in Shark Bay Microbial Mats.

Microbial mats are geobiological multilayered ecosystems that have significant evolutionary value in understanding the evolution of early life on Earth. Shark Bay, Australia has some of the best examples of modern microbial mats thriving under harsh conditions of high temperatures, salinity, desiccation, and ultraviolet (UV) radiation. Microorganisms living in extreme ecosystems are thought to potentially encode for secondary metabolites as a survival strategy. Many secondary metabolites are natural products encoded by a grouping of genes known as biosynthetic gene clusters (BGCs). Natural products have diverse chemical structures and functions which provide competitive advantages for microorganisms and can also have biotechnology applications. In the present study, the diversity of BGC were described in detail for the first time from Shark Bay microbial mats. A total of 1477 BGCs were detected in metagenomic data over a 20 mm mat depth horizon, with the surface layer possessing over 200 BGCs and containing the highest relative abundance of BGCs of all mat layers. Terpene and bacteriocin BGCs were highly represented and their natural products are proposed to have important roles in ecosystem function in these mat systems. Interestingly, potentially novel BGCs were detected from Heimdallarchaeota and Lokiarchaeota, two evolutionarily significant archaeal phyla not previously known to possess BGCs. This study provides new insights into how secondary metabolites from BGCs may enable diverse microbial mat communities to adapt to extreme environments.

Microorganisms Associated with the Marine Sponge Scopalina hapalia: A Reservoir of Bioactive Molecules to Slow Down the Aging Process.

Aging research aims at developing interventions that delay normal aging processes and some related pathologies. Recently, many compounds and extracts from natural products have been shown to delay aging and/or extend lifespan. Marine sponges and their associated microorganisms have been found to produce a wide variety of bioactive secondary metabolites; however, those from the Southwest of the Indian Ocean are much less studied, especially regarding anti-aging activities. In this study, the microbial diversity of the marine sponge Scopalina hapalia was investigated by metagenomic analysis. Twenty-six bacterial and two archaeal phyla were recovered from the sponge, of which the Proteobacteria phylum was the most abundant. In addition, thirty isolates from S. hapalia were selected and cultivated for identification and secondary metabolites production. The selected isolates were affiliated to the genera Bacillus, Micromonospora, Rhodoccocus, Salinispora, Aspergillus, Chaetomium, Nigrospora and unidentified genera related to the family Thermoactinomycetaceae. Crude extracts from selected microbial cultures were found to be active against seven targets i.e., elastase, tyrosinase, catalase, sirtuin 1, Cyclin-dependent kinase 7 (CDK7), Fyn kinase and proteasome. These results highlight the potential of microorganisms associated with a marine sponge from Mayotte to produce anti-aging compounds. Future work will focus on the isolation and the characterization of bioactive molecules.

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.

Microbial Communities in Permafrost Soils of Larsemann Hills, Eastern Antarctica: Environmental Controls and Effect of Human Impact.

Although ice-free areas cover only about 0.1% of Antarctica and are characterized by harsh environmental conditions, these regions provide quite diverse conditions for the soil-forming process, having various physical and geochemical properties, and also assuring different conditions for living organisms. This study is aimed to determine existing soil microbial communities, their relationship with soil parameters and the influence of anthropogenic activity in Larsemann Hills, Eastern Antarctica. The soil microbiome was investigated at different locations using 16S rRNA gene pyrosequencing. The taxonomic analysis of the soil microbiomes revealed 12 predominant bacterial and archaeal phyla—Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, Bacteroidetes, Armatimonadetes, Firmicutes, Cyanobacteria, Thaumarchaeota. Some specific phyla have been also found in sub-surface horizons of soils investigated, thus providing additional evidence of the crucial role of gravel pavement in saving the favorable conditions for both soil and microbiome development. Moreover, our study also revealed that some bacterial species might be introduced into Antarctic soils by human activities. We also assessed the effect of different soil parameters on microbial community in the harsh environmental conditions of Eastern Antarctica. pH, carbon and nitrogen, as well as fine earth content, were revealed as the most accurate predictors of soil bacterial community composition.