scholarly journals Assessing Microbial Community Patterns During Incipient Soil Formation From Basalt

2019 ◽  
Vol 124 (4) ◽  
pp. 941-958 ◽  
Author(s):  
Aditi Sengupta ◽  
James C. Stegen ◽  
Antonio A. Meira Neto ◽  
Yadi Wang ◽  
Julia W. Neilson ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Formation ◽  
Community Patterns

scholarly journals Transitory microbial habitat in the hyperarid Atacama Desert

2018 ◽  
Vol 115 (11) ◽  
pp. 2670-2675 ◽  
Author(s):  
Dirk Schulze-Makuch ◽  
Dirk Wagner ◽  
Samuel P. Kounaves ◽  
Kai Mangelsdorf ◽  
Kevin G. Devine ◽  
...  
Keyword(s):  
Microbial Community ◽  
Extreme Environments ◽  
Atacama Desert ◽  
Chemical Characterization ◽  
Soil Parameters ◽  
Rain Event ◽  
Community Patterns ◽  
Microbial Habitat ◽  
Lines Of Evidence ◽  
Active Microbial Community

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: (i) a physico-chemical characterization of the soil habitability after an exceptional rain event, (ii) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], (iii) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and (iv) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today’s extreme hyperaridity.

scholarly journals Premature neonatal gut microbial community patterns supporting an epithelial TLR-mediated pathway for necrotizing enterocolitis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Alexander G. Shaw ◽  
Kathleen Sim ◽  
Graham Rose ◽  
David J. Wooldridge ◽  
Ming-Shi Li ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bayesian Regression ◽  
Validation Dataset ◽  
Metagenomic Sequencing ◽  
Faecal Microbiota ◽  
Community Patterns ◽  
Cpg Dna ◽  
Shotgun Metagenomic Sequencing ◽  
Low Levels ◽  
Stimulation Of

Abstract Background Necrotising enterocolitis (NEC) is a devastating bowel disease, primarily affecting premature infants, with a poorly understood aetiology. Prior studies have found associations in different cases with an overabundance of particular elements of the faecal microbiota (in particular Enterobacteriaceae or Clostridium perfringens), but there has been no explanation for the different results found in different cohorts. Immunological studies have indicated that stimulation of the TLR4 receptor is involved in development of NEC, with TLR4 signalling being antagonised by the activated TLR9 receptor. We speculated that differential stimulation of these two components of the signalling pathway by different microbiota might explain the dichotomous findings of microbiota-centered NEC studies. Here we used shotgun metagenomic sequencing and qPCR to characterise the faecal microbiota community of infants prior to NEC onset and in a set of matched controls. Bayesian regression was used to segregate cases from control samples using both microbial and clinical data. Results We found that the infants suffering from NEC fell into two groups based on their microbiota; one with low levels of CpG DNA in bacterial genomes and the other with high abundances of organisms expressing LPS. The identification of these characteristic communities was reproduced using an external metagenomic validation dataset. We propose that these two patterns represent the stimulation of a common pathway at extremes; the LPS-enriched microbiome suggesting overstimulation of TLR4, whilst a microbial community with low levels of CpG DNA suggests reduction of the counterbalance to TLR4 overstimulation. Conclusions The identified microbial community patterns support the concept of NEC resulting from TLR-mediated pathways. Identification of these signals suggests characteristics of the gastrointestinal microbial community to be avoided to prevent NEC. Potential pre- or pro-biotic treatments may be designed to optimise TLR signalling.

scholarly journals Microbial community patterns in soils of the Sand fynbos

2009 ◽  
Vol 75 (2) ◽  
pp. 440-441
Author(s):  
E. Slabbert ◽  
K.J. Esler ◽  
K. Jacobs
Keyword(s):  
Microbial Community ◽  
Community Patterns

scholarly journals Changes in Functional Response of Soil Microbial Community along Chronosequence of Spontaneous Succession on Post Mining Forest Sites Evaluated by Biolog and SIR Methods

Forests ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 1005 ◽  
Author(s):  
Satoshi Kaneda ◽  
Krištůfek Václav ◽  
Petr Baldrian ◽  
Stanislav Malý ◽  
Jan Frouz
Keyword(s):  
Microbial Community ◽  
Soil Formation ◽  
Tween 80 ◽  
Culturable Bacteria ◽  
Mining Sites ◽  
Soil Microbial ◽  
Color Development ◽  
Spontaneous Succession ◽  
Forest Sites ◽  
Biolog Analysis

Soil formation in post-mining sites is crucial for restoring ecosystem function, and soil formation depend on the accumulation of soil organic matter and the development of an active microbial community. In this study, we used substrate-induced respiration (SIR) and Biolog plates to characterize microbial catabolic profiles in a chronosequence of soil samples from 15 unreclaimed post-mining sites in Sokolov, Czech Republic. The sites had been undergoing spontaneous succession for 3 to 45 years. Biolog ECO plates included 31 substrates. Of substrates used for SIR (glucose, chitin, cellulose, Tween 80, phenylethylamine, N-acetyl-D-glucosamine, L-asparagine, D-mannitol, D-galacturonic acid, α-cyclodextrin, and 4-hydroxy benzoic acid), eight were also used for the Biolog plates. Soil respiration, total bacteria number, and culturable bacteria number were also measured. The total and culturable number of bacteria increased with site age (p < 0.01 and p < 0.05, respectively). The percentage of culturable bacteria decreased with site age (p < 0.01). Biolog analysis indicated that average well-color development (AWCD), evenness, and richness increased with site age. SIR data indicated that only average activities tended to increase with site age (p = 0.06). According to redundancy analysis (RDA), the eight substrates, which were commonly used in both methods (SIR and BIOLOG) explained 74.4% of the variation of data from all Biolog substrates. Among the eight substrates common to both methods, only data for N-acetyl-D-glucosamine were positively correlated (p < 0.01) between Biolog and SIR. Both methods revealed microbial catabolic profile changed along the chronosequence. PCA indicated that site age, soil carbon, and pH were the most important drivers of microbial catabolic profiles.

scholarly journals Influence of prokaryotic microorganisms on initial soil formation along a glacier forefield on King George Island, maritime Antarctica

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Patryk Krauze ◽  
Dirk Wagner ◽  
Sizhong Yang ◽  
Diogo Spinola ◽  
Peter Kühn
Keyword(s):  
Microbial Community ◽  
Vegetation Cover ◽  
Soil Formation ◽  
Silicate Weathering ◽  
Lateral Moraine ◽  
King George Island ◽  
Maritime Antarctica ◽  
Glacier Forefield ◽  
Microbiological Methods ◽  
Soil Forming Processes

AbstractCompared to the 1970s, the edge of the Ecology Glacier on King George Island, maritime Antarctica, is positioned more than 500 m inwards, exposing a large area of new terrain to soil-forming processes and periglacial climate for more than 40 years. To gain information on the state of soil formation and its interplay with microbial activity, three hyperskeletic Cryosols (vegetation cover of 0–80%) deglaciated after 1979 in the foreland of the Ecology Glacier and a Cambic Cryosol (vegetation cover of 100%) distal to the lateral moraine deglaciated before 1956 were investigated by combining soil chemical and microbiological methods. In the upper part of all soils, a decrease in soil pH was observed, but only the Cambic Cryosol showed a clear direction of pedogenic and weathering processes, such as initial silicate weathering indicated by a decreasing Chemical Index of Alteration with depth. Differences in the development of these initial soils could be related to different microbial community compositions and vegetation coverage, despite the short distance among them. We observed—decreasing with depth—the highest bacterial abundances and microbial diversity at vegetated sites. Multiple clusters of abundant amplicon sequence variants were found depending on the site-specific characteristics as well as a distinct shift in the microbial community structure towards more similar communities at soil depths > 10 cm. In the foreland of the Ecology Glacier, the main soil-forming processes on a decadal timescale are acidification and accumulation of soil organic carbon and nitrogen, accompanied by changes in microbial abundances, microbial community compositions, and plant coverage, whereas quantifiable silicate weathering and the formation of pedogenic oxides occur on a centennial to a millennial timescale after deglaciation.

scholarly journals Aggregate sizes regulate the microbial community patterns in sandy soil profile

2021 ◽  
Author(s):  
Yifei Sun ◽  
Meiling Sun ◽  
Guowei Chen ◽  
Xin Chen ◽  
Baoguo Li ◽  
...  
Keyword(s):  
Microbial Community ◽  
Sandy Soil ◽  
Soil Profile ◽  
Community Patterns

scholarly journals Depth-Resolved Quantification of Anaerobic Toluene Degraders and Aquifer Microbial Community Patterns in Distinct Redox Zones of a Tar Oil Contaminant Plume

2007 ◽  
Vol 74 (3) ◽  
pp. 792-801 ◽  
Author(s):  
Christian Winderl ◽  
Bettina Anneser ◽  
Christian Griebler ◽  
Rainer U. Meckenstock ◽  
Tillmann Lueders
Keyword(s):  
Microbial Community ◽  
Natural Attenuation ◽  
Hot Spot ◽  
Spatial Correlations ◽  
Community Patterns ◽  
Gradient Zone ◽  
Degradation Processes ◽  
Tightly Coupled ◽  
Tar Oil ◽  
Benzylsuccinate Synthase

ABSTRACT Microbial degradation is the only sustainable component of natural attenuation in contaminated groundwater environments, yet its controls, especially in anaerobic aquifers, are still poorly understood. Hence, putative spatial correlations between specific populations of key microbial players and the occurrence of respective degradation processes remain to be unraveled. We therefore characterized microbial community distribution across a high-resolution depth profile of a tar oil-impacted aquifer where benzene, toluene, ethylbenzene, and xylene (BTEX) degradation depends mainly on sulfate reduction. We conducted depth-resolved terminal restriction fragment length polymorphism fingerprinting and quantitative PCR of bacterial 16S rRNA and benzylsuccinate synthase genes (bssA) to quantify the distribution of total microbiota and specific anaerobic toluene degraders. We show that a highly specialized degrader community of microbes related to known deltaproteobacterial iron and sulfate reducers (Geobacter and Desulfocapsa spp.), as well as clostridial fermenters (Sedimentibacter spp.), resides within the biogeochemical gradient zone underneath the highly contaminated plume core. This zone, where BTEX compounds and sulfate—an important electron acceptor—meet, also harbors a surprisingly high abundance of the yet-unidentified anaerobic toluene degraders carrying the previously detected F1-cluster bssA genes (C. Winderl, S. Schaefer, and T. Lueders, Environ. Microbiol. 9:1035-1046, 2007). Our data suggest that this biogeochemical gradient zone is a hot spot of anaerobic toluene degradation. These findings show that the distribution of specific aquifer microbiota and degradation processes in contaminated aquifers are tightly coupled, which may be of value for the assessment and prediction of natural attenuation based on intrinsic aquifer microbiota.

scholarly journals Premature Neonatal Gut Microbial Community Patterns Supporting An Epithelial TLR-Mediated Pathway For Necrotizing Enterocolitis

2021 ◽  
Author(s):  
Alexander G Shaw ◽  
Kathleen Sim ◽  
Graham Rose ◽  
David J. Wooldridge ◽  
Ming-Shi Li ◽  
...  
Keyword(s):  
Microbial Community ◽  
Validation Dataset ◽  
Metagenomic Sequencing ◽  
Faecal Microbiota ◽  
Community Patterns ◽  
Cpg Dna ◽  
Shotgun Metagenomic Sequencing ◽  
Low Levels ◽  
Gut Microbial Community ◽  
Stimulation Of

Abstract Background: Necrotising enterocolitis (NEC) is a devastating bowel disease, primarily affecting premature infants, with a poorly understood aetiology. Prior studies have found associations in different cases with an overabundance of particular elements of the faecal microbiota (in particular Enterobacteriaceae or Clostridium perfringens), but there has been no explanation for the different results found in different cohorts. Immunological studies have indicated that stimulation of the TLR4 receptor is involved in development of NEC, with TLR4 signalling being antagonised by the activated TLR9 receptor. We speculated that differential stimulation of these two components of the signalling pathway by different microbiota might explain the dichotomous findings of microbiota-centered NEC studies. Here we used shotgun metagenomic sequencing and qPCR to characterise the faecal microbiota community of infants prior to NEC onset and in a set of matched controls. Logistic regression was used to segregate cases from control samples using both microbial and clinical data.Results: We found that the infants suffering from NEC fell into two groups based on their microbiota; one with relatively low levels of CpG DNA in bacterial genomes and the other with high abundances of organisms expressing LPS. The identification of these characteristic communities was reproduced using an external metagenomic validation dataset. We suggest that these two patterns represent the stimulation of a common pathway at extremes; the LPS leading to overstimulation of TLR4, whilst low levels of CpG fail to sufficiently stimulate TLR9. Conclusions: The identified microbial community patterns support the concept of NEC resulting from TLR-mediated pathways. Identification of these signals suggests characteristics of the gastrointestinal microbial community to be avoided to prevent NEC. Potential pre- or pro-biotic treatments may be designed to optimise TLR signalling.

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