scholarly journals Culturing of “Unculturable” Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria From Groundwater

2020 ◽  
Vol 11 ◽  
Author(s):  
Xiaoqin Wu ◽  
Sarah Spencer ◽  
Sara Gushgari-Doyle ◽  
Mon Oo Yee ◽  
Jana Voriskova ◽  
...  
Keyword(s):  
Distinct Species ◽  
Bacterial Isolates ◽  
Culture Collections ◽  
Microbial Physiology ◽  
Cell Lysate ◽  
Bacterial Cell Lysate ◽  
Organic Carbon Source ◽  
Complex Carbon ◽  
And Function ◽  
Terrestrial Subsurface

Recovery and cultivation of diverse environmentally-relevant microorganisms from the terrestrial subsurface remain a challenge despite recent advances in modern molecular technology. Here, we applied complex carbon (C) sources, i.e., sediment dissolved organic matter (DOM) and bacterial cell lysate, to enrich groundwater microbial communities for 30 days. As comparisons, we also included enrichments amended with simple C sources including glucose, acetate, benzoate, oleic acid, cellulose, and mixed vitamins. Our results demonstrate that complex C is far more effective in enriching diverse and distinct microorganisms from groundwater than simple C. Simple C enrichments yield significantly lower biodiversity, and are dominated by few phyla (e.g., Proteobacteria and Bacteroidetes), while microcosms enriched with complex C demonstrate significantly higher biodiversity including phyla that are poorly represented in published culture collections (e.g., Verrucomicrobia, Planctomycetes, and Armatimonadetes). Subsequent isolation from complex C enrichments yielded 228 bacterial isolates representing five phyla, 17 orders, and 56 distinct species, including candidate novel, rarely cultivated, and undescribed organisms. Results from this study will substantially advance cultivation and isolation strategies for recovering diverse and novel subsurface microorganisms. Obtaining axenic representatives of “once-unculturable” microorganisms will enhance our understanding of microbial physiology and function in different biogeochemical niches of terrestrial subsurface ecosystems.

scholarly journals Culturing of ‘Unculturable’ Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria from Groundwater

2020 ◽  
Author(s):  
Xiaoqin Wu ◽  
Sarah Spencer ◽  
Sara Gushgari-Doyle ◽  
Mon Oo Yee ◽  
Jana Voriskova ◽  
...  
Keyword(s):  
Oleic Acid ◽  
Organic Carbon ◽  
Microbial Communities ◽  
Bacterial Cell ◽  
Distinct Species ◽  
Organic C ◽  
Cell Lysate ◽  
Bacterial Cell Lysate ◽  
Diverse Field ◽  
Terrestrial Subsurface

ABSTRACTThe recovery and cultivation of diverse field-related microorganisms from the terrestrial subsurface environment remains a challenge despite recent advances in modern molecular technology. Here we applied natural organic carbon (C), i.e., sediment-derived natural organic matter (NOM) and bacterial cell lysate, to groundwater microbial communities for a 30-day enrichment incubation, followed by conventional direct-plating for isolation. The groundwater was collected from a background well at the Oak Ridge Reservation Field Research Center, Tennessee. As a comparison, we also included enrichments amended with simple organic C sources, including glucose, acetate, benzoate, oleic acid, cellulose, and mixed vitamins. Our results demonstrate that complex natural organic C sources are more effective in enriching diverse bacterial species from groundwater than simple organic C sources. Microcosms amended with simple organic C (glucose, acetate, benzoate, or oleic acid) show significantly lower biodiversity than unamended control and are dominated by only few phyla such as Proteobacteria and Bacteroidetes. In contrast, microcosms amended with complex natural organic C (sediment NOM or bacterial cell lysate) display significantly higher biodiversity, and enrich distinct species from the phyla that are poorly represented in published culture collections (e.g., Verrucomicrobia, Planctomycetes, and Armatimonadetes). Our subsequent isolation efforts from natural organic C-amended enrichments led to 222 purified bacterial isolates representing 5 phyla, 16 orders, and 54 distinct species including candidate novel, rarely cultivated, and undescribed organisms.ImportanceInnovative strategies for recovering bacterial strains representing the true diversity of microbial communities in the terrestrial subsurface would significantly advance the understanding of ecologically critical taxa residing in these ecosystems. In this study, we demonstrate that complex natural organic C that mimic the naturally available resources for microbes encourages the growth of diverse bacteria much more robustly than traditional simplistic organic C sources. Results from this study will substantially advance and improve the design of strategies to effectively cultivate and isolate diverse and novel subsurface microorganisms in the laboratory. Obtaining axenic cultures of the ‘once-unculturable’ microorganisms will greatly enhance our understanding of microbial physiology, function, and roles in different biogeochemical niches in terrestrial subsurface ecosystems.

scholarly journals mSphere of Influence: Peering through a Keyhole into the Unseen World

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Sarah L. Lebeis
Keyword(s):  
Microbial Communities ◽  
Bacterial Isolates ◽  
Culture Collections ◽  
Link Type ◽  
And Function ◽  
Root Microbiota

ABSTRACT Sarah Lebeis studies the assembly and function of plant microbiomes. In this mSphere of Influence article, she reflects on how the paper “Functional Overlap of the Arabidopsis Leaf and Root Microbiota” (Y. Bai, D. B. Müller, G. Srinivas, R. Garrido-Oter, et al., Nature 528:364-369, 2015, https://doi.org/10.1038/nature16192) provided a roadmap for how large culture collections composed of well-characterized bacterial isolates provide essential resources to test hypotheses concerning microbial communities.

Phylogenetic Diversity and Mycotoxin Potential of Emergent Phytopathogens within the Fusarium tricinctum Species Complex

2022 ◽  
Author(s):  
Imane Laraba ◽  
Mark Busman ◽  
David M. Geiser ◽  
Kerry O'Donnell
Keyword(s):  
Species Complex ◽  
Phylogenetic Diversity ◽  
Agricultural Research ◽  
Distinct Species ◽  
Culture Collections ◽  
Strain Collection ◽  
Food And Feed ◽  
Feed Safety ◽  
Large Survey ◽  
Fusarium Tricinctum

Recent studies on multiple continents indicate members of the Fusarium tricinctum species complex (FTSC) are emerging as prevalent pathogens of small-grain cereals, pulses, and other economically important crops. These understudied fusaria produce structurally diverse mycotoxins, among which enniatins (ENNs) and moniliformin (MON) are the most frequent and of greatest concern to food and feed safety. Herein a large survey of fusaria in the Fusarium Research Center and Agricultural Research Service culture collections was undertaken to assess species diversity and mycotoxin potential within the FTSC. A 151-strain collection originating from diverse hosts and substrates from different agroclimatic regions throughout the world was selected from 460 FTSC strains to represent the breadth of FTSC phylogenetic diversity. Evolutionary relationships inferred from a 5-locus dataset, using maximum likelihood and parsimony, resolved the 151 strains as 24 phylogenetically distinct species, including nine that are new to science. Of the five genes analyzed, nearly full-length phosphate permease sequences contained the most phylogenetically informative characters, establishing its suitability for species-level phylogenetics within the FTSC. Fifteen of the species produced ENNs, MON, the sphingosine analog 2-amino-14,16- dimethyloctadecan-3-ol (AOD), and the toxic pigment aurofusarin (AUR) on a cracked corn kernel substrate. Interestingly, the five earliest diverging species in the FTSC phylogeny (i.e., F. iranicum, F. flocciferum, F. torulosum, Fusarium spp. FTSC 8 and 24) failed to produce AOD and MON, but synthesized ENNs and/or AUR. Moreover, our reassessment of nine published phylogenetic studies on the FTSC identified 11 additional novel taxa, suggesting this complex comprises at least 36 species.

scholarly journals Genome-Resolved Metagenomics Extends the Environmental Distribution of the Verrucomicrobia Phylum to the Deep Terrestrial Subsurface

mSphere ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Sophie L. Nixon ◽  
Rebecca A. Daly ◽  
Mikayla A. Borton ◽  
Lindsey M. Solden ◽  
Susan A. Welch ◽  
...  
Keyword(s):  
Hydraulic Fracturing ◽  
Genomic Analysis ◽  
Metagenomic Data ◽  
Organic Polymer ◽  
Comparative Genomic ◽  
Culture Collections ◽  
Environmental Distribution ◽  
Novel Genus ◽  
Fracturing Fluids ◽  
Terrestrial Subsurface

ABSTRACT Bacteria of the phylum Verrucomicrobia are prevalent and are particularly common in soil and freshwater environments. Their cosmopolitan distribution and reported capacity for polysaccharide degradation suggests members of Verrucomicrobia are important contributors to carbon cycling across Earth’s ecosystems. Despite their prevalence, the Verrucomicrobia are underrepresented in isolate collections and genome databases; consequently, their ecophysiological roles may not be fully realized. Here, we expand genomic sampling of the Verrucomicrobia phylum by describing a novel genus, “Candidatus Marcellius,” belonging to the order Opitutales. “Ca. Marcellius” was recovered from a shale-derived produced fluid metagenome collected 313 days after hydraulic fracturing, the deepest environment from which a member of the Verrucomicrobia has been recovered to date. We uncover genomic attributes that may explain the capacity of this organism to inhabit a shale gas well, including the potential for utilization of organic polymers common in hydraulic fracturing fluids, nitrogen fixation, adaptation to high salinities, and adaptive immunity via CRISPR-Cas. To illuminate the phylogenetic and environmental distribution of these metabolic and adaptive traits across the Verrucomicrobia phylum, we performed a comparative genomic analysis of 31 publicly available, nearly complete Verrucomicrobia genomes. Our genomic findings extend the environmental distribution of the Verrucomicrobia 2.3 kilometers into the terrestrial subsurface. Moreover, we reveal traits widely encoded across members of the Verrucomicrobia, including the capacity to degrade hemicellulose and to adapt to physical and biological environmental perturbations, thereby contributing to the expansive habitat range reported for this phylum. IMPORTANCE The Verrucomicrobia phylum of bacteria is widespread in many different ecosystems; however, its role in microbial communities remains poorly understood. Verrucomicrobia are often low-abundance community members, yet previous research suggests they play a major role in organic carbon degradation. While Verrucomicrobia remain poorly represented in culture collections, numerous genomes have been reconstructed from metagenomic data sets in recent years. The study of genomes from across the phylum allows for an extensive assessment of their potential ecosystem roles. The significance of this work is (i) the recovery of a novel genus of Verrucomicrobia from 2.3 km in the subsurface with the ability to withstand the extreme conditions that characterize this environment, and (ii) the most extensive assessment of ecophysiological traits encoded by Verrucomicrobia genomes to date. We show that members of this phylum are specialist organic polymer degraders that can withstand a wider range of environmental conditions than previously thought.

scholarly journals Bacterial Natural Product Drug Discovery for New Antibiotics: Strategies for Tackling the Problem of Antibiotic Resistance by Efficient Bioprospecting

Antibiotics ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 842
Author(s):  
Yannik K. Schneider
Keyword(s):  
Natural Products ◽  
Antibiotic Resistance ◽  
Resistance Mechanisms ◽  
Clinical Use ◽  
Bacterial Isolates ◽  
Development Of Resistance ◽  
Antimicrobial Resistance Genes ◽  
New Antibiotics ◽  
Fast Development ◽  
And Function

The problem of antibiotic resistance has become a challenge for our public health and society; it has allowed infectious diseases to re-emerge as a risk to human health. New antibiotics that are introduced to the market face the rise of resistant pathogens after a certain period of use. The relatively fast development of resistance against some antibiotics seems to be closely linked to their microbial origin and function in nature. Antibiotics in clinical use are merely products of microorganisms or derivatives of microbial products. The evolution of these antimicrobial compounds has progressed with the evolution of the respective resistance mechanisms in microbes for billions of years. Thus, antimicrobial resistance genes are present within the environment and can be taken up by pathogens through horizontal gene transfer. Natural products from bacteria are an important source of leads for drug development, and microbial natural products have contributed the most antibiotics in current clinical use. Bioprospecting for new antibiotics is a labor-intensive task as obstacles such as redetection of known compounds and low compound yields consume significant resources. The number of bacterial isolates one can theoretically investigate for new secondary metabolites is, on the other hand, immense. Therefore, the available capacity for biodiscovery should be focused on the most promising sources for chemical novelty and bioactivity, employing the appropriate scientific tools. This can be done by first looking into under- or unexplored environments for bacterial isolates and by focusing on the promising candidates to reduce the number of subjects.

Sensitive Luminometric Method for Protein Quantification in Bacterial Cell Lysate Based on Particle Adsorption and Dissociation of Chelated Europium

2012 ◽  
Vol 84 (3) ◽  
pp. 1386-1393 ◽  
Author(s):  
Sari Pihlasalo ◽  
Antti Kulmala ◽  
Anita Rozwandowicz-Jansen ◽  
Pekka Hänninen ◽  
Harri Härmä
Keyword(s):  
Bacterial Cell ◽  
Protein Quantification ◽  
Cell Lysate ◽  
Bacterial Cell Lysate ◽  
Particle Adsorption ◽  
Adsorption And Dissociation

scholarly journals A High Diversity in Chitinolytic and Chitosanolytic Species and Enzymes and Their Oligomeric Products Exist in Soil with a History of Chitin and Chitosan Exposure

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Malathi Nampally ◽  
M. B. Govinda Rajulu ◽  
Dominique Gillet ◽  
T. S. Suryanarayanan ◽  
Bruno B. Moerschbacher
Keyword(s):  
Biomedical Applications ◽  
Fungal Species ◽  
Bacterial Isolates ◽  
Bacterial Strains ◽  
Good Source ◽  
Fungal Isolates ◽  
Reliable Performance ◽  
History Of ◽  
Chitin And Chitosan ◽  
And Function

Chitin is one of the most abundant biomolecules on earth, and its partially de-N-acetylated counterpart, chitosan, is one of the most promising biotechnological resources due to its diversity in structure and function. Recently, chitin and chitosan modifying enzymes (CCMEs) have gained increasing interest as tools to engineer chitosans with specific functions and reliable performance in biotechnological and biomedical applications. In a search for novel CCME, we isolated chitinolytic and chitosanolytic microorganisms from soils with more than ten-years history of chitin and chitosan exposure and screened them for chitinase and chitosanase isoenzymes as well as for their patterns of oligomeric products by incubating their secretomes with chitosan polymers. Of the 60 bacterial strains isolated, only eight were chitinolytic and/or chitosanolytic, while 20 out of 25 fungal isolates were chitinolytic and/or chitosanolytic. The bacterial isolates produced rather similar patterns of chitinolytic and chitosanolytic enzymes, while the fungal isolates produced a much broader range of different isoenzymes. Furthermore, diverse mixtures of oligosaccharides were formed when chitosan polymers were incubated with the secretomes of select fungal species. Our study indicates that soils with a history of chitin and chitosan exposure are a good source of novel CCME for chitosan bioengineering.

scholarly journals Adaptive divergence in brain composition between ecologically distinct incipient species

2016 ◽  
Author(s):  
Stephen H Montgomery ◽  
Richard M Merrill
Keyword(s):  
Brain Structure ◽  
Spatial Information ◽  
Ecological Speciation ◽  
Distinct Species ◽  
Adaptive Divergence ◽  
Species Pair ◽  
Incipient Species ◽  
Brain Structure And Function ◽  
Sensory Structures ◽  
And Function

During ecological speciation diverging populations are exposed to contrasting sensory and spatial information that present new behavioral and perceptive challenges. Here, we investigate how brain composition evolves during the early stages of speciation. The incipient species pair, Heliconius erato cyrbia and H. himera, have parapatric ranges across an environmental and altitudinal gradient. Despite continuing gene-flow, these species have divergent ecological, behavioral and physiological traits. We demonstrate that these incipient species also differ significantly in brain composition, especially in the size of sensory structures. H. erato has larger visual components whilst H. himera invests more heavily in olfaction. These differences are not explained by environmentally-induced plasticity, but reflect non-allometric shifts in brain structure. Our results suggest the adaptive evolution of brain structure and function play an important role in facilitating the emergence of ecologically distinct species, and imply that plasticity alone may be insufficient to meet the demands of novel environments.

The fumarylacetoacetate hydrolase (FAH) superfamily of enzymes: multifunctional enzymes from microbes to mitochondria

2018 ◽  
Vol 46 (2) ◽  
pp. 295-309 ◽  
Author(s):  
Alexander K.H. Weiss ◽  
Johannes R. Loeffler ◽  
Klaus R. Liedl ◽  
Hubert Gstach ◽  
Pidder Jansen-Dürr
Keyword(s):  
Aromatic Compounds ◽  
Metabolic Pathways ◽  
Carbon Sources ◽  
Oxaloacetate Decarboxylase ◽  
Molecular Studies ◽  
Multifunctional Enzymes ◽  
Complex Carbon ◽  
Fumarylacetoacetate Hydrolase ◽  
And Function ◽  
Regulatory Functions

Prokaryotic and eukaryotic fumarylacetoacetate hydrolase (FAH) superfamily members, sharing conserved regions that form the so-called FAH-domain, catalyze a remarkable variety of reactions. These enzymes are essential in the metabolic pathways to degrade aromatic compounds in prokaryotes and eukaryotes. It appears that prokaryotic FAH superfamily members evolved mainly to allow microbes to generate energy and useful metabolites from complex carbon sources. We review recent findings, indicating that both prokaryotic and eukaryotic members of the FAH superfamily also display oxaloacetate decarboxylase (ODx) activity. The identification of human FAH domain-containing protein 1 as mitochondrial ODx regulating mitochondrial function supports the new concept that, during evolution, eukaryotic FAH superfamily members have acquired important regulatory functions beyond catabolism of complex carbon sources. Molecular studies on the evolution and function of FAH superfamily members are expected to provide new mechanistic insights in their physiological roles.

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