Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities

AbstractQuantifying the relative contributions of microbial species to ecosystem functioning is challenging, because of the distinct mechanisms associated with microbial phylogenetic and metabolic diversity. We constructed bacterial communities with different diversity traits and employed exoenzyme activities (EEAs) and total available carbon (TAC) from substrates as proxies of bacterial functioning to test the independent effects of these two aspects of biodiversity. We expected that metabolic diversity, but not phylogenetic diversity would be associated with greater ecological function. Phylogenetically relatedness should intensify species interactions and coexistence, therefore amplifying the influence of metabolic diversity. We examined the effects of each diversity treatment using linear models, while controlling for the other, and found that phylogenetic diversity strongly influenced community functioning, positively and negatively. Metabolic diversity, however, exhibited negative or non-significant relationships with community functioning. When controlling for different substrates, EEAs increased along with phylogenetic diversity but decreased with metabolic diversity. The strength of diversity effects was related to substrate chemistry and the molecular mechanisms associated with each substrate’s degradation. EEAs of phylogenetically similar groups were strongly affected by within-genus interactions. These results highlight the unique flexibility of microbial metabolic functions that must be considered in further ecological theory development.

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Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities

FEMS Microbiology Ecology ◽

10.1093/femsec/fiab017 ◽

2021 ◽

Vol 97 (3) ◽

Author(s):

Constantinos Xenophontos ◽

Martin Taubert ◽

W Stanley Harpole ◽

Kirsten Küsel

Keyword(s):

Bacterial Communities ◽

Species Interactions ◽

Phylogenetic Diversity ◽

Molecular Mechanisms ◽

Linear Models ◽

Theory Development ◽

Metabolic Diversity ◽

Community Functioning ◽

Metabolic Functions ◽

Independent Effects

ABSTRACT Quantifying the relative contributions of microbial species to ecosystem functioning is challenging, because of the distinct mechanisms associated with microbial phylogenetic and metabolic diversity. We constructed bacterial communities with different diversity traits and employed exoenzyme activities (EEAs) and carbon acquisition potential (CAP) from substrates as proxies of bacterial functioning to test the independent effects of these two aspects of biodiversity. We expected that metabolic diversity, but not phylogenetic diversity would be associated with greater ecological function. Phylogenetically relatedness should intensify species interactions and coexistence, therefore amplifying the influence of metabolic diversity. We examined the effects of each diversity treatment using linear models, while controlling for the other, and found that phylogenetic diversity strongly influenced community functioning, positively and negatively. Metabolic diversity, however, exhibited negative or non-significant relationships with community functioning. When controlling for different substrates, EEAs increased along with phylogenetic diversity but decreased with metabolic diversity. The strength of diversity effects was related to substrate chemistry and the molecular mechanisms associated with each substrate's degradation. EEAs of phylogenetically similar groups were strongly affected by within-genus interactions. These results highlight the unique flexibility of microbial metabolic functions that must be considered in further ecological theory development.

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Specialized metabolic functions of keystone taxa sustain soil microbiome stability

Microbiome ◽

10.1186/s40168-020-00985-9 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Weibing Xun ◽

Yunpeng Liu ◽

Wei Li ◽

Yi Ren ◽

Wu Xiong ◽

...

Keyword(s):

Functional Traits ◽

Bacterial Communities ◽

Phylogenetic Diversity ◽

Soil Microbiome ◽

Ecosystem Stability ◽

Machine Learning Classification ◽

Metabolic Functions ◽

The Stability ◽

The Relationship ◽

Taxonomic Annotation

Abstract Background The relationship between biodiversity and soil microbiome stability remains poorly understood. Here, we investigated the impacts of bacterial phylogenetic diversity on the functional traits and the stability of the soil microbiome. Communities differing in phylogenetic diversity were generated by inoculating serially diluted soil suspensions into sterilized soil, and the stability of the microbiome was assessed by detecting community variations under various pH levels. The taxonomic features and potential functional traits were detected by DNA sequencing. Results We found that bacterial communities with higher phylogenetic diversity tended to be more stable, implying that microbiomes with higher biodiversity are more resistant to perturbation. Functional gene co-occurrence network and machine learning classification analyses identified specialized metabolic functions, especially “nitrogen metabolism” and “phosphonate and phosphinate metabolism,” as keystone functions. Further taxonomic annotation found that keystone functions are carried out by specific bacterial taxa, including Nitrospira and Gemmatimonas, among others. Conclusions This study provides new insights into our understanding of the relationships between soil microbiome biodiversity and ecosystem stability and highlights specialized metabolic functions embedded in keystone taxa that may be essential for soil microbiome stability.

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Spatio-Temporal Variation of the Bacterial Communities along a Salinity Gradient within a Thalassohaline Environment (Saline di Tarquinia Salterns, Italy)

Molecules ◽

10.3390/molecules26051338 ◽

2021 ◽

Vol 26 (5) ◽

pp. 1338

Author(s):

Susanna Gorrasi ◽

Andrea Franzetti ◽

Roberto Ambrosini ◽

Francesca Pittino ◽

Marcella Pasqualetti ◽

...

Keyword(s):

Bacterial Diversity ◽

Generalized Linear Models ◽

Bacterial Communities ◽

Linear Models ◽

Salinity Gradient ◽

Sampling Site ◽

Α Diversity ◽

Spatio Temporal ◽

Abundance Variation ◽

Microbiological Aspects

The “Saline di Tarquinia” salterns have been scarcely investigated regarding their microbiological aspects. This work studied the structure and composition of their bacterial communities along the salinity gradient (from the nearby sea through different ponds). The communities showed increasing simplification of pond bacterial diversity along the gradient (particularly if compared to those of the sea). Among the 38 assigned phyla, the most represented were Proteobacteria, Actinobacteria and Bacteroidetes. Differently to other marine salterns, where at the highest salinities Bacteroidetes dominated, preponderance of Proteobacteria was observed. At the genus level the most abundant taxa were Pontimonas, Marivita, Spiribacter, Bordetella, GpVII and Lentibacter. The α-diversity analysis showed that the communities were highly uneven, and the Canonical Correspondence Analysis indicated that they were structured by various factors (sampling site, sampling year, salinity, and sampling month). Moreover, the taxa abundance variation in relation to these significant parameters were investigated by Generalized Linear Models. This work represents the first investigation of a marine saltern, carried out by a metabarcoding approach, which permitted a broad vision of the bacterial diversity, covering both a wide temporal span (two years with monthly sampling) and the entire salinity gradient (from the nearby sea up to the crystallisation ponds).

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Metabonomic-Transcriptome Integration Analysis on Osteoarthritis and Rheumatoid Arthritis

International Journal of Genomics ◽

10.1155/2020/5925126 ◽

2020 ◽

Vol 2020 ◽

pp. 1-9 ◽

Cited By ~ 1

Author(s):

Ningyang Gao ◽

Li Ding ◽

Jian Pang ◽

Yuxin Zheng ◽

Yuelong Cao ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Gap Junction ◽

Molecular Mechanisms ◽

Linear Models ◽

Principal Component ◽

Enrichment Analysis ◽

Pathway Enrichment Analysis ◽

Nf Kappa B ◽

Linear Module ◽

Hedgehog Acyltransferase

Purpose. This study is aimed at exploring the potential metabolite/gene biomarkers, as well as the differences between the molecular mechanisms, of osteoarthritis (OA) and rheumatoid arthritis (RA). Methods. Transcriptome dataset GSE100786 was downloaded to explore the differentially expressed genes (DEGs) between OA samples and RA samples. Meanwhile, metabolomic dataset MTBLS564 was downloaded and preprocessed to obtain metabolites. Then, the principal component analysis (PCA) and linear models were used to reveal DEG-metabolite relations. Finally, metabolic pathway enrichment analysis was performed to investigate the differences between the molecular mechanisms of OA and RA. Results. A total of 976 DEGs and 171 metabolites were explored between OA samples and RA samples. The PCA and linear module analysis investigated 186 DEG-metabolite interactions including Glycogenin 1- (GYG1-) asparagine_54, hedgehog acyltransferase- (HHAT-) glucose_70, and TNF receptor-associated factor 3- (TRAF3-) acetoacetate_35. Finally, the KEGG pathway analysis showed that these metabolites were mainly enriched in pathways like gap junction, phagosome, NF-kappa B, and IL-17 pathway. Conclusions. Genes such as HHAT, GYG1, and TRAF3, as well as metabolites including glucose, asparagine, and acetoacetate, might be implicated in the pathogenesis of OA and RA. Metabolites like ethanol and tyrosine might participate differentially in OA and RA progression via the gap junction pathway and phagosome pathway, respectively. TRAF3-acetoacetate interaction may be involved in regulating inflammation in OA and RA by the NF-kappa B and IL-17 pathway.

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From the Andes to the desert: First overview of the bacterial community in the Rimac river, the main source of water for Lima, Peru

10.1101/2020.08.16.252965 ◽

2020 ◽

Author(s):

Pedro E. Romero ◽

Erika Calla-Quispe ◽

Camila Castillo-Vilcahuaman ◽

Mateo Yokoo ◽

Hammerly Lino Fuentes-Rivera ◽

...

Keyword(s):

Metropolitan Area ◽

Bacterial Communities ◽

Geographical Location ◽

Microbiological Quality ◽

Amplicon Sequencing ◽

Urban Sewage ◽

16S Rrna Amplicon Sequencing ◽

The Andes ◽

Metabolic Functions ◽

Quality Assessments

AbstractBackgroundThe Rimac river is the main source of water for Lima, Peru’s capital megacity. The river is constantly affected by different types of contamination including mine tailings in the Andes and urban sewage in the metropolitan area. We aim to produce the first characterization of bacterial communities in the Rimac river using a 16S rRNA amplicon sequencing approach which would be useful to identify bacterial diversity and potential understudied pathogens.ResultsWe report a higher diversity in bacterial communities from the Upper and, especially, Middle Rimac compared to the Lower Rimac (Metropolitan zone). Samples were generally grouped according to their geographical location. Bacterial classes Alphaproteobacteria, Bacteroidia, Campylobacteria, Fusobacteriia, and Gammaproteobacteria were the most frequent along the river. Arcobacter cryaerophilus (Campylobacteria) was the most frequent species in the Lower Rimac while Flavobacterium succinicans (Bacteroidia) and Hypnocyclicus (Fusobacteriia) were the most predominant in the Upper Rimac. Predicted metabolic functions in the microbiota include bacterial motility, quorum sensing and xenobiotics metabolism. Additional metabolomic analyses showed the presence natural flavonoids and antibiotics in the Upper Rimac, and herbicides in the Lower Rimac.ConclusionsThe dominance in the Metropolitan area of Arcobacter cryaerophilus, an emergent pathogen associated with fecal contamination and antibiotic multiresistance, but that is not usually reported in traditional microbiological quality assessments, highlights the necessity to apply next-generation sequencing tools to improve pathogen surveillance. We believe that our study will encourage the integration of omics sciences in Peru and its application on current environmental and public health issues.

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Targeting MDM2-dependent serine metabolism as a therapeutic strategy for liposarcoma

Science Translational Medicine ◽

10.1126/scitranslmed.aay2163 ◽

2020 ◽

Vol 12 (547) ◽

pp. eaay2163

Author(s):

Madi Y. Cissé ◽

Samuel Pyrdziak ◽

Nelly Firmin ◽

Laurie Gayte ◽

Maud Heuillet ◽

...

Keyword(s):

Therapeutic Strategy ◽

Molecular Mechanisms ◽

De Novo ◽

Negative Regulator ◽

Nucleotide Synthesis ◽

Metabolic Functions ◽

Xenograft Models ◽

Well Differentiated ◽

Serine Metabolism

Well-differentiated and dedifferentiated liposarcomas (LPSs) are characterized by a systematic amplification of the MDM2 oncogene, which encodes a key negative regulator of the p53 pathway. The molecular mechanisms underlying MDM2 overexpression while sparing wild-type p53 in LPS remain poorly understood. Here, we show that the p53-independent metabolic functions of chromatin-bound MDM2 are exacerbated in LPS and mediate an addiction to serine metabolism that sustains nucleotide synthesis and tumor growth. Treatment of LPS cells with Nutlin-3A, a pharmacological inhibitor of the MDM2-p53 interaction, stabilized p53 but unexpectedly enhanced MDM2-mediated control of serine metabolism by increasing its recruitment to chromatin, likely explaining the poor clinical efficacy of this class of MDM2 inhibitors. In contrast, genetic or pharmacological inhibition of chromatin-bound MDM2 by SP141, a distinct MDM2 inhibitor triggering its degradation, or interfering with de novo serine synthesis, impaired LPS growth both in vitro and in clinically relevant patient-derived xenograft models. Our data indicate that targeting MDM2 functions in serine metabolism represents a potential therapeutic strategy for LPS.

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Gut Microbiota as Important Mediator Between Diet and DNA Methylation and Histone Modifications in the Host

Nutrients ◽

10.3390/nu12030597 ◽

2020 ◽

Vol 12 (3) ◽

pp. 597 ◽

Cited By ~ 2

Author(s):

Patrizia D’Aquila ◽

Laurie Lynn Carelli ◽

Francesco De Rango ◽

Giuseppe Passarino ◽

Dina Bellizzi

Keyword(s):

Dna Methylation ◽

Gut Microbiota ◽

Histone Modifications ◽

Molecular Mechanisms ◽

Current Evidence ◽

Long Term Effects ◽

Metabolic Functions ◽

Complex Ecosystem ◽

Short And Long Term ◽

And Function

The human gut microbiota is a complex ecosystem consisting of trillions of microorganisms that inhabit symbiotically on and in the human intestine. They carry out, through the production of a series of metabolites, many important metabolic functions that complement the activity of mammalian enzymes and play an essential role in host digestion. Interindividual variability of microbiota structure, and consequently of the expression of its genes (microbiome), was largely ascribed to the nutritional regime. Diet influences microbiota composition and function with short- and long-term effects. In spite of the vast literature, molecular mechanisms underlying these effects still remain elusive. In this review, we summarized the current evidence on the role exerted by gut microbiota and, more specifically, by its metabolites in the establishment of the host epigenome. The interest in this topic stems from the fact that, by modulating DNA methylation and histone modifications, the gut microbiota does affect the cell activities of the hosting organism.

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Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms

mSystems ◽

10.1128/msystems.00299-20 ◽

2020 ◽

Vol 5 (4) ◽

Cited By ~ 3

Author(s):

Elizabeth A. McDaniel ◽

Benjamin D. Peterson ◽

Sarah L. R. Stevens ◽

Patricia Q. Tran ◽

Karthik Anantharaman ◽

...

Keyword(s):

Phylogenetic Diversity ◽

Large Scale ◽

Carbon Fixation ◽

Anaerobic Bacteria ◽

Inorganic Mercury ◽

Metal Resistance ◽

Metabolic Flexibility ◽

Metabolic Diversity ◽

Content Type ◽

Methylmercury Production

ABSTRACT Methylmercury is a potent bioaccumulating neurotoxin that is produced by specific microorganisms that methylate inorganic mercury. Methylmercury production in diverse anaerobic bacteria and archaea was recently linked to the hgcAB genes. However, the full phylogenetic and metabolic diversity of mercury-methylating microorganisms has not been fully unraveled due to the limited number of cultured experimentally verified methylators and the limitations of primer-based molecular methods. Here, we describe the phylogenetic diversity and metabolic flexibility of putative mercury-methylating microorganisms by hgcAB identification in publicly available isolate genomes and metagenome-assembled genomes (MAGs) as well as novel freshwater MAGs. We demonstrate that putative mercury methylators are much more phylogenetically diverse than previously known and that hgcAB distribution among genomes is most likely due to several independent horizontal gene transfer events. The microorganisms we identified possess diverse metabolic capabilities spanning carbon fixation, sulfate reduction, nitrogen fixation, and metal resistance pathways. We identified 111 putative mercury methylators in a set of previously published permafrost metatranscriptomes and demonstrated that different methylating taxa may contribute to hgcA expression at different depths. Overall, we provide a framework for illuminating the microbial basis of mercury methylation using genome-resolved metagenomics and metatranscriptomics to identify putative methylators based upon hgcAB presence and describe their putative functions in the environment. IMPORTANCE Accurately assessing the production of bioaccumulative neurotoxic methylmercury by characterizing the phylogenetic diversity, metabolic functions, and activity of methylators in the environment is crucial for understanding constraints on the mercury cycle. Much of our understanding of methylmercury production is based on cultured anaerobic microorganisms within the Deltaproteobacteria, Firmicutes, and Euryarchaeota. Advances in next-generation sequencing technologies have enabled large-scale cultivation-independent surveys of diverse and poorly characterized microorganisms from numerous ecosystems. We used genome-resolved metagenomics and metatranscriptomics to highlight the vast phylogenetic and metabolic diversity of putative mercury methylators and their depth-discrete activities in thawing permafrost. This work underscores the importance of using genome-resolved metagenomics to survey specific putative methylating populations of a given mercury-impacted ecosystem.

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Comprehensive Analysis of Differential Immunocyte Infiltration and Potential ceRNA Networks Involved in the Development of Atrial Fibrillation

BioMed Research International ◽

10.1155/2020/8021208 ◽

2020 ◽

Vol 2020 ◽

pp. 1-10

Author(s):

Jiafeng Wu ◽

Huiming Deng ◽

Qianghua Chen ◽

Qiang Wu ◽

Xiaolong Li ◽

...

Keyword(s):

Atrial Fibrillation ◽

Dna Methylation ◽

Left Atrial ◽

Molecular Mechanisms ◽

Linear Models ◽

Core Gene ◽

Differential Analysis ◽

Methylation Analysis ◽

Protein Protein Interaction ◽

Dna Methylation Analysis

This study is aimed at identifying potential molecular mechanisms and candidate biomarkers in the left atrial regions for the diagnosis and treatment of valvular atrial fibrillation (VAF). Multibioinformatics methods, including linear models for microarray analysis (LIMMA), an SVA algorithm, CIBERSORT immune infiltration, and DNA methylation analysis, were employed. In addition, the protein-protein interaction (PPI) network, Gene Ontology (GO), and molecular pathways of differentially expressed genes (DEGs) or differential methylation regions were constructed. In all, compared with the normal rhythm group, 243 different mRNAs (29 downregulated and 214 upregulated) and 26 different lncRNAs (3 downregulated and 23 upregulated) were detected in the left atrium (LA) of atrial fibrillation (AF) patients, and the neutrophil and CD8+ T cell were infiltrated. Additionally, 199 different methylation sites (107 downregulated and 92 upregulated) were also identified based on DNA methylation analysis. After integration, ELOVL2, CCR2, and WEE1 were detected for differentially methylated and differentially transcribed genes. Among them, WEE1 was also a core gene identified by the competing endogenous RNA (ceRNA) network that included WEE1-KRBOX1-AS1-hsa-miR-17-5p, in VAF left atrial tissue. We combined the DNA methylation and transcriptional expression differential analysis and found that WEE1 (cg13365543) may well be a candidate gene regulated by DNA methylation modification. Moreover, KRBOX1-AS1 and WEE1 can compete endogenously and may mediate myocardial tissue infiltration into CD8+ T cells and participate in the AF process.

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