scholarly journals 309 metagenome assembled microbial genomes from deep sediment samples in the Gulfs of Kathiawar Peninsula

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Neelam M. Nathani ◽  
Kaushambee J. Dave ◽  
Priyanka P. Vatsa ◽  
Mayur S. Mahajan ◽  
Parth Sharma ◽  
...  
Keyword(s):  
Arabian Sea ◽  
Anthropogenic Activities ◽  
Ecological Niches ◽  
Microbial Genomes ◽  
Deep Sediment ◽  
Bacterial Phyla ◽  
Metagenomics Data ◽  
Deep Sediments ◽  
Sediment Microbes

AbstractProkaryoplankton genomes from the deep marine sediments are less explored compared to shallow shore sediments. The Gulfs of Kathiawar peninsula experience varied currents and inputs from different on-shore activities. Any perturbations would directly influence the microbiome and their normal homeostasis. Advancements in reconstructing genomes from metagenomes allows us to understand the role of individual unculturable microbes in ecological niches like the Gulf sediments. Here, we report 309 bacterial and archaeal genomes assembled from metagenomics data of deep sediments from sites in the Gulf of Khambhat and Gulf of Kutch as well as a sample from the Arabian Sea. Phylogenomics classified them into 5 archaeal and 18 bacterial phyla. The genomes will facilitate understanding of the physiology, adaptation and impact of on-shore anthropogenic activities on the deep sediment microbes.

scholarly journals A widely distributed hydrogenase oxidises atmospheric H2 during bacterial growth

2020 ◽  
Vol 14 (11) ◽  
pp. 2649-2658 ◽  
Author(s):  
Zahra F. Islam ◽  
Caitlin Welsh ◽  
Katherine Bayly ◽  
Rhys Grinter ◽  
Gordon Southam ◽  
...  
Keyword(s):  
Physiological Role ◽  
Pcr Analysis ◽  
Ecological Niches ◽  
Bacterial Phyla ◽  
Oxidation Rates ◽  
Biochemical Assays ◽  
Phylogenomic Analyses ◽  
Phylogenetic Lineages ◽  
And Control

Abstract Diverse aerobic bacteria persist by consuming atmospheric hydrogen (H2) using group 1h [NiFe]-hydrogenases. However, other hydrogenase classes are also distributed in aerobes, including the group 2a [NiFe]-hydrogenase. Based on studies focused on Cyanobacteria, the reported physiological role of the group 2a [NiFe]-hydrogenase is to recycle H2 produced by nitrogenase. However, given this hydrogenase is also present in various heterotrophs and lithoautotrophs lacking nitrogenases, it may play a wider role in bacterial metabolism. Here we investigated the role of this enzyme in three species from different phylogenetic lineages and ecological niches: Acidithiobacillus ferrooxidans (phylum Proteobacteria), Chloroflexus aggregans (phylum Chloroflexota), and Gemmatimonas aurantiaca (phylum Gemmatimonadota). qRT-PCR analysis revealed that the group 2a [NiFe]-hydrogenase of all three species is significantly upregulated during exponential growth compared to stationary phase, in contrast to the profile of the persistence-linked group 1h [NiFe]-hydrogenase. Whole-cell biochemical assays confirmed that all three strains aerobically respire H2 to sub-atmospheric levels, and oxidation rates were much higher during growth. Moreover, the oxidation of H2 supported mixotrophic growth of the carbon-fixing strains C. aggregans and A. ferrooxidans. Finally, we used phylogenomic analyses to show that this hydrogenase is widely distributed and is encoded by 13 bacterial phyla. These findings challenge the current persistence-centric model of the physiological role of atmospheric H2 oxidation and extend this process to two more phyla, Proteobacteria and Gemmatimonadota. In turn, these findings have broader relevance for understanding how bacteria conserve energy in different environments and control the biogeochemical cycling of atmospheric trace gases.

scholarly journals A widely distributed hydrogenase oxidises atmospheric H2 during bacterial growth

2020 ◽  
Author(s):  
Zahra F. Islam ◽  
Caitlin Welsh ◽  
Katherine Bayly ◽  
Rhys Grinter ◽  
Gordon Southam ◽  
...  
Keyword(s):  
Physiological Role ◽  
Pcr Analysis ◽  
Ecological Niches ◽  
Bacterial Phyla ◽  
Oxidation Rates ◽  
Biochemical Assays ◽  
Phylogenomic Analyses ◽  
Phylogenetic Lineages ◽  
And Control

AbstractDiverse aerobic bacteria persist by consuming atmospheric hydrogen (H2) using group 1h [NiFe]-hydrogenases. However, other hydrogenase classes are also distributed in aerobes, including the group 2a [NiFe]-hydrogenase. Based on studies focused on Cyanobacteria, the reported physiological role of the group 2a [NiFe]-hydrogenase is to recycle H2 produced by nitrogenase. However, given this hydrogenase is also present in various heterotrophs and lithoautotrophs lacking nitrogenases, it may play a wider role in bacterial metabolism. Here we investigated the role of this enzyme in three species from different phylogenetic lineages and ecological niches: Acidithiobacillus ferrooxidans (phylum Proteobacteria), Chloroflexus aggregans (phylum Chloroflexota), and Gemmatimonas aurantiaca (phylum Gemmatimonadota). qRT-PCR analysis revealed that the group 2a [NiFe]-hydrogenase of all three species is significantly upregulated during exponential growth compared to stationary phase, in contrast to the profile of the persistence-linked group 1h [NiFe]-hydrogenase. Whole-cell biochemical assays confirmed that all three strains aerobically respire H2 to sub-atmospheric levels, and oxidation rates were much higher during growth. Moreover, the oxidation of H2 supported mixotrophic growth of the carbon-fixing strains C. aggregans and A. ferrooxidans. Finally, we used phylogenomic analyses to show that this hydrogenase is widely distributed and is encoded by 13 bacterial phyla. These findings challenge the current persistence-centric model of the physiological role of atmospheric H2 oxidation and extends this process to two more phyla, Proteobacteria and Gemmatimonadota. In turn, these findings have broader relevance for understanding how bacteria conserve energy in different environments and control the biogeochemical cycling of atmospheric trace gases.

scholarly journals Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Sharon A. Huws ◽  
Joan E. Edwards ◽  
Wanchang Lin ◽  
Francesco Rubino ◽  
Mark Alston ◽  
...  
Keyword(s):  
Energy Harvesting ◽  
Perennial Ryegrass ◽  
Transcriptional Activity ◽  
Ecological Niches ◽  
Ecological Interactions ◽  
Carbohydrate Degradation ◽  
Host Nutrition ◽  
Role Based ◽  
Insight Into

Abstract Background Gut microbiomes, such as the rumen, greatly influence host nutrition due to their feed energy-harvesting capacity. We investigated temporal ecological interactions facilitating energy harvesting at the fresh perennial ryegrass (PRG)-biofilm interface in the rumen using an in sacco approach and prokaryotic metatranscriptomic profiling. Results Network analysis identified two distinct sub-microbiomes primarily representing primary (≤ 4 h) and secondary (≥ 4 h) colonisation phases and the most transcriptionally active bacterial families (i.e Fibrobacteriaceae, Selemondaceae and Methanobacteriaceae) did not interact with either sub-microbiome, indicating non-cooperative behaviour. Conversely, Prevotellaceae had most transcriptional activity within the primary sub-microbiome (focussed on protein metabolism) and Lachnospiraceae within the secondary sub-microbiome (focussed on carbohydrate degradation). Putative keystone taxa, with low transcriptional activity, were identified within both sub-microbiomes, highlighting the important synergistic role of minor bacterial families; however, we hypothesise that they may be ‘cheating’ in order to capitalise on the energy-harvesting capacity of other microbes. In terms of chemical cues underlying transition from primary to secondary colonisation phases, we suggest that AI-2-based quorum sensing plays a role, based on LuxS gene expression data, coupled with changes in PRG chemistry. Conclusions In summary, we show that fresh PRG-attached prokaryotes are resilient and adapt quickly to changing niches. This study provides the first major insight into the complex temporal ecological interactions occurring at the plant-biofilm interface within the rumen. The study also provides valuable insights into potential plant breeding strategies for development of the utopian plant, allowing optimal sustainable production of ruminants.

scholarly journals Defining the niche for niche construction: evolutionary and ecological niches

2021 ◽  
Vol 36 (3) ◽  
Author(s):  
Rose Trappes
Keyword(s):  
Evolutionary Biology ◽  
Ecological Niche ◽  
Niche Construction ◽  
Habitat Degradation ◽  
Ecological Niches ◽  
Niche Concept ◽  
Definition Of ◽  
Compare And Contrast ◽  
Extreme Habitat

AbstractNiche construction theory (NCT) aims to transform and unite evolutionary biology and ecology. Much of the debate about NCT has focused on construction. Less attention has been accorded to the niche: what is it, exactly, that organisms are constructing? In this paper I compare and contrast the definition of the niche used in NCT with ecological niche definitions. NCT’s concept of the evolutionary niche is defined as the sum of selection pressures affecting a population. So defined, the evolutionary niche is narrower than the ecological niche. Moreover, when contrasted with a more restricted ecological niche concept, it has a slightly different extension. I point out three kinds of cases in which the evolutionary niche does not coincide with realized ecological niches: extreme habitat degradation, commensalism, and non-limiting or super-abundant resources. These conceptual differences affect the role of NCT in unifying ecology and evolutionary biology.

scholarly journals Nanopore-Sequencing Characterization of the Gut Microbiota of Melolontha melolontha Larvae: Contribution to Protection against Entomopathogenic Nematodes?

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 396
Author(s):  
Ewa Sajnaga ◽  
Marcin Skowronek ◽  
Agnieszka Kalwasińska ◽  
Waldemar Kazimierczak ◽  
Karolina Ferenc ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Entomopathogenic Nematodes ◽  
Bacterial Species ◽  
Antagonistic Activity ◽  
Rrna Gene ◽  
Nanopore Sequencing ◽  
Bacterial Phyla ◽  
Melolontha Melolontha

This study focused on the potential relationships between midgut microbiota of the common cockchafer Melolontha melolontha larvae and their resistance to entomopathogenic nematodes (EPN) infection. We investigated the bacterial community associated with control and unsusceptible EPN-exposed insects through nanopore sequencing of the 16S rRNA gene. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant bacterial phyla within the complex and variable midgut microbiota of the wild M. melolontha larvae. The core microbiota was found to include 82 genera, which accounted for 3.4% of the total number of identified genera. The EPN-resistant larvae differed significantly from the control ones in the abundance of many genera belonging to the Actinomycetales, Rhizobiales, and Clostridiales orders. Additionally, the analysis of the microbiome networks revealed different sets of keystone midgut bacterial genera between these two groups of insects, indicating differences in the mutual interactions between bacteria. Finally, we detected Xenorhabdus and Photorhabdus as gut residents and various bacterial species exhibiting antagonistic activity against these entomopathogens. This study paves the way to further research aimed at unravelling the role of the host gut microbiota on the output of EPN infection, which may contribute to enhancement of the efficiency of nematodes used in eco-friendly pest management.

scholarly journals Nematode Hsp90: highly conserved but functionally diverse

Parasitology ◽  
2014 ◽  
Vol 141 (9) ◽  
pp. 1203-1215 ◽  
Author(s):  
VICTORIA GILLAN ◽  
EILEEN DEVANEY
Keyword(s):  
Life Cycle ◽  
Heat Shock Protein 90 ◽  
Ecological Niches ◽  
Actual Number ◽  
Host Organism ◽  
Free Living ◽  
Parasitic Species ◽  
Free Living Nematode ◽  
Functionally Diverse

SUMMARYNematodes are amongst the most successful and abundant organisms on the planet with approximately 30 000 species described, although the actual number of species is estimated to be one million or more. Despite sharing a relatively simple and invariant body plan, there is considerable diversity within the phylum. Nematodes have evolved to colonize most ecological niches, and can be free-living or can parasitize plants or animals to the detriment of the host organism. In this review we consider the role of heat shock protein 90 (Hsp90) in the nematode life cycle. We describe studies on Hsp90 in the free-living nematode Caenorhabditis elegans and comparative work on the parasitic species Brugia pahangi, and consider whether a dependence upon Hsp90 can be exploited for the control of parasitic species.

scholarly journals Geospatial technology perspectives for mining vis-a-vis sustainable forest ecosystems

2017 ◽  
Vol 11 (1) ◽  
pp. 219-238 ◽  
Author(s):  
Laxmi Goparaju ◽  
P. Rama Chandra Prasad ◽  
Firoz Ahmad
Keyword(s):  
Forest Ecosystems ◽  
Anthropogenic Activities ◽  
Biogeochemical Cycles ◽  
Mining Activities ◽  
Forest Environment ◽  
Mining Operations ◽  
Geospatial Technology ◽  
The Status ◽  
The Impact

Abstract Forests, the backbone of biogeochemical cycles and life supporting systems, are under severe pressure due to varied anthropogenic activities. Mining activities are one among the major reasons for forest destruction questioning the survivability and sustainability of flora and fauna existing in that area. Thus, monitoring and managing the impact of mining activities on natural resources at regular intervals is necessary to check the status of their depleted conditions, and to take up restoration and conservative measurements. Geospatial technology provides means to identify the impact of different mining operations on forest ecosystems and helps in proposing initiatives for safeguarding the forest environment. In this context, the present study highlights the problems related to mining in forest ecosystems and elucidates how geospatial technology can be employed at various stages of mining activities to achieve a sustainable forest ecosystem. The study collates information from various sources and highlights the role of geospatial technology in mining industries and reclamation process.

scholarly journals Influence of Metal-Resistant Staphylococcus aureus Strain K1 on the Alleviation of Chromium Stress in Wheat

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1354 ◽  
Author(s):  
Fanrong Zeng ◽  
Munazza Zahoor ◽  
Muhammad Waseem ◽  
Alia Anayat ◽  
Muhammad Rizwan ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Staphylococcus Aureus ◽  
Anthropogenic Activities ◽  
Toxic Metal ◽  
Triticum Aestivum L ◽  
Aureus Strain ◽  
Peat Moss ◽  
Cr Toxicity ◽  
Living Organisms

Chromium (Cr) is recognized as a toxic metal that has detrimental effects on living organisms; notably, it is discharged into soil by various industries as a result of anthropogenic activities. Microbe-assisted phytoremediation is one of the most emergent and environmentally friendly methods used for the detoxification of pollutants. In this study, the alleviative role of Staphylococcus aureus strain K1 was evaluated in wheat (Triticum aestivum L.) under Cr stress. For this, various Cr concentrations (0, 25, 50 and 100 mg·kg−1) with and without peat-moss-based bacterial inoculum were applied in the soil. Results depicted that Cr stress reduced the plants’ growth by causing oxidative stress in the absence of S. aureus K1 inoculation. However, the application of S. aureus K1 regulated the plants’ growth and antioxidant enzymatic activities by reducing oxidative stress and Cr toxicity through conversion of Cr6+ to Cr3+. The Cr6+ uptake by wheat was significantly reduced in the S. aureus K1 inoculated plants. It can be concluded that the application of S. aureus K1 could be an effective approach to alleviate the Cr toxicity in wheat and probably in other cereals grown under Cr stress.

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