Microbial contamination screening and interpretation for biological laboratory environments

AbstractAdvances in microbiome researches have led us to the realization that the composition of microbial communities of indoor environment is profoundly affected by the function of buildings, and in turn may bring detrimental effects to the indoor environment and the occupants. Thus investigation is warranted for a deeper understanding of the potential impact of the indoor microbial communities. Among these environments, the biological laboratories stand out because they are relatively clean and yet are highly susceptible to microbial contaminants. In this study, we assessed the microbial compositions of samples from the surfaces of various sites across different types of biological laboratories. We have qualitatively and quantitatively assessed these possible microbial contaminants, and found distinct differences in their microbial community composition. We also found that the type of laboratories has a larger influence than the sampling site in shaping the microbial community, in terms of both structure and richness. On the other hand, the public areas of the different types of laboratories share very similar sets of microbes. Tracing the main sources of these microbes, we identified both environmental and human factors that are important factors in shaping the diversity and dynamics of these possible microbial contaminations in biological laboratories. These possible microbial contaminants that we have identified will be helpful for people who aim to eliminate them from samples.ImportanceMicrobial communities from biological laboratories might hamper the conduction of molecular biology experiments, yet these possible contaminations are not yet carefully investigated. In this work, a metagenomic approach has been applied to identify the possible microbial contaminants and their sources, from the surfaces of various sites across different types of biological laboratories. We have found distinct differences in their microbial community compositions. We have also identified the main sources of these microbes, as well as important factors in shaping the diversity and dynamics of these possible microbial contaminations. The identification and interpretation of these possible microbial contaminants in biological laboratories would be helpful for alleviate their potential detrimental effects.

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Microbial communities in soil macro-aggregates respire less, are more diverse and stable across successional and geographical gradients

10.5194/egusphere-egu21-16011 ◽

2021 ◽

Author(s):

Daquan Sun ◽

Gerrit Angst ◽

Jan Frouz

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Microbial Respiration ◽

Soil Aggregates ◽

Sampling Site ◽

Microbial Community Composition ◽

Dominant Factor ◽

Community Stability ◽

Community Structures ◽

Soil Fractions

<p>The stability of soil organic carbon is empirically believed to relate to the location of soil microorganisms inside or between aggregates. However, there are knowledge gaps about how micro-niches shape the microbial community composition and activity and how these effects vary between various soils. Here, we investigate fungal and bacterial community structures (composition and biomass), networks, and respiration in individual micro-niches between and inside soil aggregates using seven different chronosequences (both primary and secondary successions covering sites from pioneer stages to well-developed ecosystems) from a maritime climate in Belgium to a more continental climate in Hungary. We show that while the sampling site is the most crucial factor in shaping microbial community structures, soil aggregates are often more important than succession age and vegetation in differentiating major microbial taxa. Soil fractions are also the dominant factor affecting microbial biomass along the individual chronosequences. Specifically, macro-aggregates often have more variable &#945;-diversities and high microbial community stability, accompanied by low microbial respiration rates. Although the other isolated soil fractions have similar microbial diversities as macro-aggregates, they feature unstable microbial communities with a higher respiration rate. The isolated primary particles have more stable bacterial communities in secondary than primary successions. We, thus, provide a mechanism for interpreting the links between soil microsite heterogeneity, microbial community stability, and microbial respiration.&#160;</p>

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Collection of a Bacterial Community Reconstructed from Marine Metagenomes Derived from Jinhae Bay, South Korea

Data ◽

10.3390/data6050044 ◽

2021 ◽

Vol 6 (5) ◽

pp. 44

Author(s):

Jae-Hyun Lim ◽

Il-Nam Kim

Keyword(s):

Microbial Community ◽

South Korea ◽

Microbial Communities ◽

Marine Bacteria ◽

Sampling Site ◽

Community Change ◽

Rrna Gene ◽

Water Column Stratification ◽

Metagenomics Data ◽

Jinhae Bay

Marine bacteria are known to play significant roles in marine biogeochemical cycles regarding the decomposition of organic matter. Despite the increasing attention paid to the study of marine bacteria, research has been too limited to fully elucidate the complex interaction between marine bacterial communities and environmental variables. Jinhae Bay, the study area in this work, is the most anthropogenically eutrophied coastal bay in South Korea, and while its physical and biogeochemical characteristics are well described, less is known about the associated changes in microbial communities. In the present study, we reconstructed a metagenomics data based on the 16S rRNA gene to investigate temporal and vertical changes in microbial communities at three depths (surface, middle, and bottom) during a seven-month period from June to December 2016 at one sampling site (J1) in Jinhae Bay. Of all the bacterial data, Proteobacteria, Bacteroidetes, and Cyanobacteria were predominant from June to November, whereas Firmicutes were predominant in December, especially at the middle and bottom depths. These results show that the composition of the microbial community is strongly associated with temporal changes. Furthermore, the community compositions were markedly different between the surface, middle, and bottom depths in summer, when water column stratification and bottom water hypoxia (low dissolved oxygen level) were strongly developed. Metagenomics data contribute to improving our understanding of important relationships between environmental characteristics and microbial community change in eutrophication-induced and deoxygenated coastal areas.

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Responses of soil microbial communities and enzyme activities to nitrogen and phosphorus additions in Chinese fir plantations of subtropical China

Biogeosciences Discussions ◽

10.5194/bgd-12-10359-2015 ◽

2015 ◽

Vol 12 (13) ◽

pp. 10359-10387 ◽

Cited By ~ 4

Author(s):

W. Y. Dong ◽

X. Y. Zhang ◽

X. Y. Liu ◽

X. L. Fu ◽

F. S. Chen ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Enzyme Activities ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

Chinese Fir ◽

Subtropical China ◽

Nitrogen And Phosphorus ◽

Soil Microbial ◽

Nutrient Additions

Abstract. Nitrogen (N) and phosphorus (P) additions to forest ecosystems are known to influence various above-ground properties, such as plant productivity and composition, and below-ground properties, such as soil nutrient cycling. However, our understanding of how soil microbial communities and their functions respond to nutrient additions in subtropical plantations is still not complete. In this study, we added N and P to Chinese fir plantations in subtropical China to examine how nutrient additions influenced soil microbial community composition and enzyme activities. The results showed that most soil microbial properties were responsive to N and/or P additions, but responses often varied depending on the nutrient added and the quantity added. For instance, there were more than 30 % greater increases in the activities of β-Glucosidase (βG) and N-acetyl-β-D-glucosaminidase (NAG) in the treatments that received nutrient additions compared to the control plot, whereas acid phosphatase (aP) activity was always higher (57 and 71 %, respectively) in the P treatment. N and P additions greatly enhanced the PLFA abundanceespecially in the N2P treatment, the bacterial PLFAs (bacPLFAs), fungal PLFAs (funPLFAs) and actinomycic PLFAs (actPLFAs) were about 2.5, 3 and 4 times higher, respectively, than in the CK. Soil enzyme activities were noticeably higher in November than in July, mainly due to seasonal differences in soil moisture content (SMC). βG or NAG activities were significantly and positively correlated with microbial PLFAs. There were also significant relationships between gram-positive (G+) bacteria and all three soil enzymes. These findings indicate that G+ bacteria is the most important microbial community in C, N, and P transformations in Chinese fir plantations, and that βG and NAG would be useful tools for assessing the biogeochemical transformation and metabolic activity of soil microbes. We recommend combined additions of N and P fertilizer to promote soil fertility and microbial activity in this kind of plantation.

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Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity

Frontiers in Microbiology ◽

10.3389/fmicb.2021.616730 ◽

2021 ◽

Vol 12 ◽

Author(s):

Scott F. George ◽

Noah Fierer ◽

Joseph S. Levy ◽

Byron Adams

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Environmental Conditions ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

Vapor Flow ◽

Arid Soils ◽

Opposite Pattern ◽

Dry Valley

Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5–10 km2) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.

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Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms

Microorganisms ◽

10.3390/microorganisms9071495 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1495

Author(s):

Tim Piel ◽

Giovanni Sandrini ◽

Gerard Muyzer ◽

Corina P. D. Brussaard ◽

Pieter C. Slot ◽

...

Keyword(s):

Hydrogen Peroxide ◽

Microbial Community ◽

Microbial Communities ◽

Microbial Community Composition ◽

Glycoside Hydrolases ◽

Microbial Community Analysis ◽

Cyanobacterial Blooms ◽

Temporary Increase ◽

Low Concentrations ◽

Harmful Cyanobacterial Blooms

Applying low concentrations of hydrogen peroxide (H2O2) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H2O2, little is known about the impacts of these H2O2 treatments on other members of the microbial community. In this study, we investigated changes in microbial community composition during two lake treatments with low H2O2 concentrations (target: 2.5 mg L−1) and in two series of controlled lake incubations. The results show that the H2O2 treatments effectively suppressed the dominant cyanobacteria Aphanizomenon klebahnii, Dolichospermum sp. and, to a lesser extent, Planktothrix agardhii. Microbial community analysis revealed that several Proteobacteria (e.g., Alteromonadales, Pseudomonadales, Rhodobacterales) profited from the treatments, whereas some bacterial taxa declined (e.g., Verrucomicrobia). In particular, the taxa known to be resistant to oxidative stress (e.g., Rheinheimera) strongly increased in relative abundance during the first 24 h after H2O2 addition, but subsequently declined again. Alpha and beta diversity showed a temporary decline but recovered within a few days, demonstrating resilience of the microbial community. The predicted functionality of the microbial community revealed a temporary increase of anti-ROS defenses and glycoside hydrolases but otherwise remained stable throughout the treatments. We conclude that the use of low concentrations of H2O2 to suppress cyanobacterial blooms provides a short-term pulse disturbance but is not detrimental to lake microbial communities and their ecosystem functioning.

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Soil microbial communities in microaggregates are less affected by top-down effects of collembolans than those in macroaggregates

10.5194/egusphere-egu21-10345 ◽

2021 ◽

Author(s):

Amandine Erktan ◽

MD Ekramul Haque ◽

Jérôme Cortet ◽

Paul Henning Krogh ◽

Stefan Scheu

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Trophic Interactions ◽

Phospholipid Fatty Acid ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

Trophic Levels ◽

Soil Matrix ◽

Fungal Abundance

<p>Trophic regulation of microbial communities is receiving growing interest in soil ecology. Most studies investigated the effect of higher trophic levels on microbial communities at the bulk soil level. However, microbes are not equally accessible to consumers. They may be hidden in small pores and thus protected from consumers, suggesting that trophic regulation may depend on the localization of microbes within the soil matrix. As microaggregates (< 250 &#181;m) usually are more stable than macroaggregates (> 250 &#181;m) and embedded in the latter, we posit that they will be less affected by trophic regulations than larger aggregates. We quantified the effect of four contrasting species of collembolans (Ceratophysella denticulata, Protaphorura fimata, Folsomia candida, Sinella curviseta) on the microbial community composition in macro- (250 &#181;m &#8211; 2mm) and microaggregates (50 &#8211; 250 &#181;m). To do so, we re-built consumer-prey systems comprising remaining microbial background (post-autoclaving), fungal prey (Chaetomium globosum), and collembolan species (added as single species or combined). After three months, we quantified microbial community composition using phospholipid fatty acid markers (PLFAs). We found that the microbial communities in macroaggregates were more affected by the addition of collembolans than the communities in microaggregates. In particular, the fungal-to-bacterial (F:B) ratio significantly decreased in soil macroaggregates in the presence of collembolans. In the microaggregates, the F:B ratio remained lower and unaffected by collembolan inoculation. Presumably, fungal hyphae were more abundant in macroaggregates because they offered more habitat space for them, and the collembolans reduced fungal abundance because they consumed them. On the contrary, microaggregates presumably contained microbial communities protected from consumers. In addition, collembolans increased the formation of macroaggregates but did not influence their stability, despite their negative effect on fungal abundance, a well-known stabilizing agent. Overall, we show that trophic interactions between microbial communities and collembolans depend on the aggregate size class considered and, in return, soil macroaggregation is affected by these trophic interactions.</p>

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Microbiota community assembly in wild rice (Oryza longistaminata) in response to drought stress shows phylogenetic conservation, stochasticity, and aboveground-belowground patterns

10.21203/rs.3.rs-40339/v1 ◽

2020 ◽

Author(s):

xia ding ◽

Xiaojue Peng ◽

Zhichao Chen ◽

Yingjie Li ◽

Lihui Mao ◽

...

Keyword(s):

Microbial Community ◽

Drought Stress ◽

Microbial Communities ◽

Community Assembly ◽

Wild Rice ◽

Microbial Community Composition ◽

Α Diversity ◽

Oryza Longistaminata ◽

Network Properties ◽

Microbiome Assembly

Abstract Background Drought is a global environmental stress that limits crop yields. Microbial communities control many biogeochemical processes, and a predictive understanding of how crop microbial communities assemble in response to drought stress is central to addressing the challenges caused by drought. Little is known about the microbiome assembly processes in rice-ecosystems, particularly with regard to their environmental adaptation. Wild rice may serve as a source of superior drought tolerance candidate for rice breeding. There is an urgent need to explore wild rice resistance mechanisms to drought stress. Here, we evaluated the effect of drought stress on the microbial community recruitment and assembly in the endosphere (leaf, stem, and root) and rhizosphere of Oryza longistaminata. Results Species replacement was the dominant process shaping microbial community composition under drought stress. O. longistaminata recruited the phyla Actinobacteria and Fusobacteria, the genus Streptomyces, and phototrophic prokaryotes to improve its fitness. The host exerted strong effects on microbiome assembly, and the responses of the microbial community structure to the drought environment showed above- and belowground patterns. Drought reduced taxonomic α-diversity and destabilized co-occurrence network properties in the leaves and stems, but not in the roots and rhizosphere. Drought promoted the restructuring and strengthening of belowground network links to more strongly interconnect network properties. The drought response of the microbiome was phylogenetically conserved. Stochastic (neutral) processes acted on microbial community reassembly in response to drought stress across all four compartments. Conclusions Our results provide new insight into the mechanisms through which drought alters microbial community assembly in drought-tolerant wild rice and reveal a potential strategy for manipulating plant microbiomes to improve crop fitness.

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Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence

Applied and Environmental Microbiology ◽

10.1128/aem.02646-18 ◽

2019 ◽

Vol 85 (7) ◽

Cited By ~ 17

Author(s):

Alexander Burkert ◽

Thomas A. Douglas ◽

Mark P. Waldrop ◽

Rachel Mackelprang

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Microbial Communities ◽

Community Composition ◽

Environmental Conditions ◽

Microbial Community Composition ◽

Rrna Gene ◽

Subzero Temperatures ◽

Dormant Cells

ABSTRACTPermafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the classBacilliwere more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of theClostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCEPermafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.

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Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil

Scientific Reports ◽

10.1038/s41598-019-52148-y ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 11

Author(s):

Vanessa L. Brisson ◽

Jennifer E. Schmidt ◽

Trent R. Northen ◽

John P. Vogel ◽

Amélie C. M. Gaudin

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Microbial Community Composition ◽

Microbial Community Analysis ◽

Agricultural System ◽

Community Members ◽

Genetic Groups ◽

Maize Domestication ◽

Rhizosphere Microbial Community

Abstract Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines’ rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.

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Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities

mBio ◽

10.1128/mbio.02776-19 ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 4

Author(s):

Paul Carini ◽

Manuel Delgado-Baquerizo ◽

Eve-Lyn S. Hinckley ◽

Hannah Holland‐Moritz ◽

Tess E. Brewer ◽

...

Keyword(s):

Microbial Community ◽

Spatial Variability ◽

Spatial Heterogeneity ◽

Microbial Communities ◽

Temporal Variability ◽

Temporal Dynamics ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

Environmental Preferences ◽

Soil Microbial

ABSTRACT Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes. IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.

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