Carbon metabolic profiling of Trichoderma strains provides insight into potential ecological niches

Mycologia ◽  
2020 ◽  
Vol 112 (2) ◽  
pp. 213-223
Author(s):  
Chao Wang ◽  
Wen-Ying Zhuang
Keyword(s):  
Metabolic Profiling ◽  
Ecological Niches ◽  
Insight Into

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 Unearthing the Boreal Soil Resistome Associated with Permafrost Thaw

2020 ◽  
Author(s):  
Tracie J. Haan ◽  
Devin M. Drown
Keyword(s):  
Antibiotic Resistance ◽  
Active Layer ◽  
Resistance Genes ◽  
Soil Bacteria ◽  
Bacterial Community Composition ◽  
Ecological Niches ◽  
Whole Genome ◽  
Near Surface ◽  
Permafrost Thaw ◽  
Insight Into

ABSTRACTUnderstanding the distribution and mobility of antibiotic resistance genes (ARGs) in soil bacteria from diverse ecological niches is critical in assessing their impacts on the global spread of antibiotic resistance. In permafrost associated soils, climate and human driven forces augment near-surface thaw altering the overlying active layer. Physiochemical changes shift bacterial community composition and metabolic functioning, however, it is unknown if permafrost thaw will affect ARGs comprising the boreal soil resistome. To assess how thaw shifts the resistome, we performed susceptibility testing and whole genome sequencing on soil isolates from a disturbance-induced thaw gradient in Interior Alaska. We found resistance was widespread in the Alaskan isolates, with 87% of the 90 isolates resistant to at least one of the five antibiotics. We also observed positive trends in both the proportion of resistant isolates and the abundance of ARGs with permafrost thaw. However, the number of ARGs per genome and types of genes present were shown to cluster more strongly by bacterial taxa rather than thaw emphasizing the evolutionary origins of resistance and the role vertical gene transfer has in shaping the predominantly chromosomally encoded ARGs. The observed higher proportion of plasmid-borne and distinct ARGs in our isolates compared to RefSoil+ suggests local conditions affect the composition of the resistome along with selection for ARG mobility. Overall taxonomy and geography shape the resistome, suggesting that as microbial communities shift in response to permafrost thaw so will the ARGs in the boreal active layer.IMPORTANCEAs antibiotic resistance continues to emerge and rapidly spread in clinical settings, it is imperative to generate studies that build insight into the ecology of environmental resistance genes that pose a threat to human health. This study provides insight into the occurrence of diverse ARGs found in Alaskan soil bacteria which is suggestive of the potential to compromise health. The observed differences in ARG abundance with increasing permafrost thaw suggest the role of soil disturbance in driving the distribution of resistant determinants and the predominant taxa that shape the resistome. Moreover, the high-quality whole genome assemblies generated in this study are an extensive resource for microbial researchers interested in permafrost thaw and will provide a steppingstone for future research into ARG mobility and transmission risks.

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

2021 ◽  
Author(s):  
Sharon 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 BackgroundGut 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. ResultsNetwork analysis identified two distinct sub-microbiomes primarily representing primary (<4h) and secondary (>4h) 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. ConclusionsIn 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 Bridging the Gap Between Mammal and Insect Ears – A Comparative and Evolutionary View of Sound-Reception

2021 ◽  
Vol 9 ◽  
Author(s):  
Ben Warren ◽  
Manuela Nowotny
Keyword(s):  
Ecological Niches ◽  
Body Parts ◽  
Molecular Processes ◽  
Research Fields ◽  
Evolutionary Context ◽  
Animal Phyla ◽  
Sound Reception ◽  
Evolutionary View ◽  
Common Principle ◽  
Insight Into

Insects must wonder why mammals have ears only in their head and why they evolved only one common principle of ear design—the cochlea. Ears independently evolved at least 19 times in different insect groups and therefore can be found in completely different body parts. The morphologies and functional characteristics of insect ears are as wildly diverse as the ecological niches they exploit. In both, insects and mammals, hearing organs are constrained by the same biophysical principles and their respective molecular processes for mechanotransduction are thought to share a common evolutionary origin. Due to this, comparative knowledge of hearing across animal phyla provides crucial insight into fundamental processes of auditory transduction, especially at the biomechanical and molecular level. This review will start by comparing hearing between insects and mammals in an evolutionary context. It will then discuss current findings about sound reception will help to bridge the gap between both research fields.

Metabolic profiling study of shikonin's cytotoxic activity in the Huh7 human hepatoma cell line

2017 ◽  
Vol 13 (5) ◽  
pp. 841-851 ◽  
Author(s):  
E. D. Spyrelli ◽  
A. V. Kyriazou ◽  
C. Virgiliou ◽  
A. Nakas ◽  
O. Deda ◽  
...  
Keyword(s):  
Cytotoxic Activity ◽  
Metabolic Profiling ◽  
Hepatoma Cell ◽  
Hepatoma Cell Line ◽  
Human Hepatoma ◽  
Human Hepatoma Cell ◽  
Huh7 Cells ◽  
First Time ◽  
Line P ◽  
Insight Into

Metabolic profiling employed for the first time on Huh7 cells upon treatment with shikonin could provide insight into the metabolic perturbations induced by shikonin.

scholarly journals Microbiomes Attached to Fresh Perennial Ryegrass- are Temporally Resilient and Adapt to Changing Ecological Niches

2020 ◽  
Author(s):  
Sharon 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 BackgroundGut 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. ResultsNetwork analysis identified two distinct sub-microbiomes primarily representing primary (<4h) and secondary (>4h) 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. ConclusionsIn 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 New Insight into Antimicrobial Compounds from Food and Marine-Sourced Carnobacterium Species through Phenotype and Genome Analyses

2020 ◽  
Vol 8 (7) ◽  
pp. 1093
Author(s):  
Simon Begrem ◽  
Flora Ivaniuk ◽  
Frédérique Gigout-Chevalier ◽  
Laetitia Kolypczuk ◽  
Sandrine Bonnetot ◽  
...  
Keyword(s):  
Polyketide Synthase ◽  
Biosynthetic Gene Cluster ◽  
Ecological Niches ◽  
Antimicrobial Compounds ◽  
Biosynthetic Gene ◽  
Peptide Synthetase ◽  
Seafood Products ◽  
Genome Analyses ◽  
Encoding Genes ◽  
Insight Into

Carnobacterium maltaromaticum and Carnobacterium divergens, isolated from food products, are lactic acid bacteria known to produce active and efficient bacteriocins. Other species, particularly those originating from marine sources, are less studied. The aim of the study is to select promising strains with antimicrobial potential by combining genomic and phenotypic approaches on large datasets comprising 12 Carnobacterium species. The biosynthetic gene cluster (BGCs) diversity of 39 publicly available Carnobacterium spp. genomes revealed 67 BGCs, distributed according to the species and ecological niches. From zero to six BGCs were predicted per strain and classified into four classes: terpene, NRPS (non-ribosomal peptide synthetase), NRPS-PKS (hybrid non-ribosomal peptide synthetase-polyketide synthase), RiPP (ribosomally synthesized and post-translationally modified peptide). In parallel, the antimicrobial activity of 260 strains from seafood products was evaluated. Among the 60% of active strains, three genomes were sequenced and submitted to a dereplication process. C. inhibens MIP2551 produced a high amountof H2O2, probably thanks to the presence of four oxidase-encoding genes. C. maltaromaticum EBP3019 and SF668 strains were highly efficient against Listeria monocytogenes. A new extracellular 16 kDa unmodified bacteriocin in the EBP3019 strain and five different bacteriocins in SF668 were highlighted. In this study, the overview of antimicrobial BGC and inhibitory activities of Carnobacterium spp. allowed the prediction of potential innovative natural products that could be relevant for biotechnological applications.

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

2020 ◽  
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

AbstractGut 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. Network analysis identified two distinct sub-microbiomes primarily representing primary (≤4h) and secondary (≥4h) 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. In summary, this study provides the first major insight into the complex temporal ecological interactions occurring at the plant-biofilm interface within the rumen.

scholarly journals Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Phani Rama Krishna Behra ◽  
B. M. Fredrik Pettersson ◽  
Malavika Ramesh ◽  
Santanu Dasgupta ◽  
Leif A. Kirsebom
Keyword(s):  
Tap Water ◽  
Sigma Factors ◽  
Ecological Niches ◽  
Mrna Levels ◽  
Secretion Systems ◽  
Mycobacterium Neoaurum ◽  
Rnaseq Data ◽  
Genes Encoding ◽  
Insight Into ◽  
Mycobacterium Mucogenicum

AbstractNontuberculous mycobacteria, NTM, are of growing concern and among these members of the Mycobacterium mucogenicum (Mmuc) and Mycobacterium neoaurum (Mneo) clades can cause infections in humans and they are resistant to first-line anti-tuberculosis drugs. They can be isolated from different ecological niches such as soil, tap water and ground water. Mycobacteria, such as Mmuc and Mneo, are classified as rapid growing mycobacteria, RGM, while the most familiar, Mycobacterium tuberculosis, belongs to the slow growing mycobacteria, SGM. Modern “omics” approaches have provided new insights into our understanding of the biology and evolution of this group of bacteria. Here we present comparative genomics data for seventeen NTM of which sixteen belong to the Mmuc- and Mneo-clades. Focusing on virulence genes, including genes encoding sigma/anti-sigma factors, serine threonine protein kinases (STPK), type VII (ESX genes) secretion systems and mammalian cell entry (Mce) factors we provide insight into their presence as well as phylogenetic relationship in the case of the sigma/anti-sigma factors and STPKs. Our data further suggest that these NTM lack ESX-5 and Mce2 genes, which are known to affect virulence. In this context, Mmuc- and Mneo-clade members lack several of the genes in the glycopeptidolipid (GLP) locus, which have roles in colony morphotype appearance and virulence. For the M. mucogenicum type strain, MmucT, we provide RNASeq data focusing on mRNA levels for sigma factors, STPK, ESX proteins and Mce proteins. These data are discussed and compared to in particular the SGM and fish pathogen Mycobacterium marinum. Finally, we provide insight into as to why members of the Mmuc- and Mneo-clades show resistance to rifampin and isoniazid, and why MmucT forms a rough colony morphotype.

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