Temporal variation in soil bacterial communities can be confounded with spatial variation

ABSTRACT Investigating temporal variation in soil bacterial communities advances our fundamental understanding of the causal processes driving biological variation, and how the composition of these important ecosystem members may change into the future. Despite this, temporal variation in soil bacteria remains understudied, and the effects of spatial heterogeneity in bacterial communities on the detection of temporal changes is largely unknown. Using 16S rRNA gene amplicon sequencing, we evaluated temporal patterns in soil bacterial communities from indigenous forest and human-impacted sites sampled repeatedly over a 5-year period. Temporal variation appeared to be greater when fewer spatial samples per site were analysed, as well as in human-impacted compared to indigenous sites (P < 0.01 for both). The biggest portion of variation in bacterial community richness and composition was explained by soil physicochemical variables (13–24%) rather than spatial distance or sampling time (<1%). These results highlight the importance of adequate spatiotemporal replication when sampling soil communities for environmental monitoring, and the importance of conducting temporal research across a wide variety of land uses. This will ensure we have a true understanding of how bacterial communities change over space and time; the work presented here provides important considerations for how such research should be designed.

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Impact of Maize–Mushroom Intercropping on the Soil Bacterial Community Composition in Northeast China

Agronomy ◽

10.3390/agronomy10101526 ◽

2020 ◽

Vol 10 (10) ◽

pp. 1526

Author(s):

Xiaoqin Yang ◽

Yang Wang ◽

Luying Sun ◽

Xiaoning Qi ◽

Fengbin Song ◽

...

Keyword(s):

Bacterial Communities ◽

Northeast China ◽

Management Practice ◽

Bacterial Community Composition ◽

Soil Microbial Communities ◽

Chemical Properties ◽

Crop Productivity ◽

Rrna Gene ◽

Soil Bacterial Communities ◽

Soil Bacterial

Conservative agricultural practices have been adopted to improve soil quality and maintain crop productivity. An efficient intercropping of maize with mushroom has been developed in Northeast China. The objective of this study was to evaluate and compare the effects of planting patterns on the diversity and structure of the soil bacterial communities at a 0–20 cm depth in the black soil zone of Northeast China. The experiment consisted of monoculture of maize and mushroom, and intercropping in a split-plot arrangement. The characteristics of soil microbial communities were performed by 16S rRNA gene amplicom sequencing. The results showed that intercropping increased soil bacterial richness and diversity compared with maize monoculture. The relative abundances of Acidobacteria, Chloroflexi, Saccharibacteria and Planctomycetes were significantly higher, whereas Proteobacteria and Firmicutes were lower in intercropping than maize monoculture. Redundancy analysis suggested that pH, NO3−-N and NH4+-N contents had a notable effect on the structure of the bacterial communities. Moreover, intercropping significantly increased the relative abundance of carbohydrate metabolism pathway functional groups. Overall, these findings demonstrated that intercropping of maize with mushroom strongly impacts the physical and chemical properties of soil as well as the diversity and structure of the soil bacterial communities, suggesting this is a sustainable agricultural management practice in Northeast China.

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Field-Scale Transplantation Experiment To Investigate Structures of Soil Bacterial Communities at Pioneering Sites

Applied and Environmental Microbiology ◽

10.1128/aem.05778-11 ◽

2011 ◽

Vol 77 (23) ◽

pp. 8241-8248 ◽

Cited By ~ 30

Author(s):

Anna Lazzaro ◽

Andreas Gauer ◽

Josef Zeyer

Keyword(s):

Bacterial Community ◽

Environmental Conditions ◽

Bacterial Communities ◽

Seasonal Pattern ◽

Dry Weight ◽

Rrna Gene ◽

Soil Bacterial Communities ◽

Reciprocal Transplantation ◽

Temperature And Precipitation ◽

Soil Bacterial

ABSTRACTStudies on the effect of environmental conditions on plants and microorganisms are a central issue in ecology, and they require an adequate experimental setup. A strategy often applied in geobotanical studies is based on the reciprocal transplantation of plant species at different sites. We adopted a similar approach as a field-based tool to investigate the relationships of soil bacterial communities with the environment. Soil samples from two different (calcareous and siliceous) unvegetated glacier forefields were reciprocally transplanted and incubated for 15 months between 2009 and 2010. Controls containing local soils were included. The sites were characterized over time in terms of geographical (bedrock, exposition, sunlight, temperature, and precipitation) and physicochemical (texture, water content, soluble and nutrients) features. The incubating local (“home”) and transplanted (“away”) soils were monitored for changes in extractable nutrients and in the bacterial community structure, defined through terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA gene. Concentrations of soluble ions in most samples were more significantly affected by seasons than by the transplantation. For example, NO3−showed a seasonal pattern, increasing from 1 to 3 μg NO3−(g soil dry weight)−1after the melting of snow but decreasing to <1 μg NO3−(g soil dry weight)−1in autumn. Seasons, and in particular strong precipitation events occurring in the summer of 2010 (200 to 300 mm of rain monthly), were also related to changes of bacterial community structures. Our results show the suitability of this approach to compare responses of bacterial communities to different environmental conditions directly in the field.

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Soil Bacterial Communities and Diversity in Alpine Grasslands on the Tibetan Plateau Based on 16S rRNA Gene Sequencing

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.630722 ◽

2021 ◽

Vol 9 ◽

Author(s):

Hongmao Jiang ◽

Youchao Chen ◽

Yang Hu ◽

Ziwei Wang ◽

Xuyang Lu

Keyword(s):

Tibetan Plateau ◽

Bacterial Communities ◽

Soil Bacteria ◽

Alpine Grassland ◽

Rrna Gene ◽

The Tibetan Plateau ◽

Alpine Grasslands ◽

Soil Bacterial Communities ◽

Soil Bacterial ◽

Grassland Types

The Tibetan Plateau, widely known as the world’s “Third Pole,” has gained extensive attention due to its susceptibility to climate change. Alpine grasslands are the dominant ecosystem on the Tibetan Plateau, albeit little is known about the microbial community and diversity among different alpine grassland types. Here, soil bacterial composition and diversity in the upper soils of five alpine grassland ecosystems, alpine meadow (AM), alpine steppe (AS), alpine meadow steppe (AMS), alpine desert (AD), and alpine desert steppe (ADS), were investigated based on the 16S rRNA gene sequencing technology. Actinobacteria (46.12%) and Proteobacteria (29.67%) were the two dominant soil bacteria at the phylum level in alpine grasslands. There were significant differences in the relative abundance at the genus level among the five different grassland types, especially for the Rubrobacter, Solirubrobacter, Pseudonocardia, Gaiella, Haliangium, and Geodermatophilus. Six alpha diversity indices were calculated based on the operational taxonomic units (OTUs), including Good’s coverage index, phylogenetic diversity (PD) whole tree index, Chao1 index, observed species index, Shannon index, and Simpson index. The Good’s coverage index value was around 0.97 for all the grassland types in the study area, meaning the soil bacteria samplings sequenced sufficiently. No statistically significant difference was shown in other diversity indices’ value, indicating the similar richness and evenness of soil bacteria in these alpine grasslands. The beta diversity, represented by Bray–Curtis dissimilarity and the non-metric multidimensional scaling (NMDS), showed that OTUs were clustered within alpine grasslands, indicating a clear separation of soil bacterial communities. In addition, soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), pH, and soil water content (SWC) were closely related to the variations in soil bacterial compositions. These results indicated that soil bacterial taxonomic compositions were similar, while soil bacterial community structures were different among the five alpine grassland types. The environmental conditions, including SOM, TN, TP, pH, and SWC, might influence the soil bacterial communities on the Tibetan Plateau.

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Microbial Diversity of Temperate Pine and Native Forest Soils Profiled by 16S rRNA Gene Amplicon Sequencing

Microbiology Resource Announcements ◽

10.1128/mra.00298-21 ◽

2021 ◽

Vol 10 (20) ◽

Author(s):

Adenike Eunice Amoo ◽

Olubukola Oluranti Babalola

Keyword(s):

Land Use ◽

Land Use Change ◽

Bacterial Communities ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Native Forest ◽

Soil Bacterial Diversity ◽

Anthropogenic Pressures ◽

Biodiversity Knowledge ◽

Soil Bacterial

ABSTRACT Most biodiversity measures indicate an ongoing deterioration due to intensifying anthropogenic pressures even though efforts are being intensified worldwide to conserve biodiversity. Knowledge of the implication of land use change on soil bacterial communities is essential for ecosystem restoration. Here, the effect of the conversion of native forests to temperate pine forests on soil bacterial diversity and community composition was investigated. The diversity and composition of the bacterial communities were affected by land use change across the sites.

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Soil Bacterial Communities Exhibit Strong Biogeographic Patterns at Fine Taxonomic Resolution

mSystems ◽

10.1128/msystems.00540-20 ◽

2020 ◽

Vol 5 (4) ◽

Cited By ~ 1

Author(s):

Sean K. Bay ◽

Melodie A. McGeoch ◽

Osnat Gillor ◽

Nimrod Wieler ◽

David J. Palmer ◽

...

Keyword(s):

Bacterial Communities ◽

Taxonomic Resolution ◽

Rrna Gene ◽

Data Sets ◽

Soil Biodiversity ◽

Biogeographic Patterns ◽

Soil Bacterial Communities ◽

Rare Biosphere ◽

Local Soil ◽

Soil Bacterial

ABSTRACT Bacteria have been inferred to exhibit relatively weak biogeographic patterns. To what extent such findings reflect true biological phenomena or methodological artifacts remains unclear. Here, we addressed this question by analyzing the turnover of soil bacterial communities from three data sets. We applied three methodological innovations: (i) design of a hierarchical sampling scheme to disentangle environmental from spatial factors driving turnover; (ii) resolution of 16S rRNA gene amplicon sequence variants to enable higher-resolution community profiling; and (iii) application of the new metric zeta diversity to analyze multisite turnover and drivers. At fine taxonomic resolution, rapid compositional turnover was observed across multiple spatial scales. Turnover was overwhelmingly driven by deterministic processes and influenced by the rare biosphere. The communities also exhibited strong distance decay patterns and taxon-area relationships, with z values within the interquartile range reported for macroorganisms. These biogeographical patterns were weakened upon applying two standard approaches to process community sequencing data: clustering sequences at 97% identity threshold and/or filtering the rare biosphere (sequences lower than 0.05% relative abundance). Comparable findings were made across local, regional, and global data sets and when using shotgun metagenomic markers. Altogether, these findings suggest that bacteria exhibit strong biogeographic patterns, but these signals can be obscured by methodological limitations. We advocate various innovations, including using zeta diversity, to advance the study of microbial biogeography. IMPORTANCE It is commonly thought that bacterial distributions show lower spatial variation than for multicellular organisms. In this article, we present evidence that these inferences are artifacts caused by methodological limitations. Through leveraging innovations in sampling design, sequence processing, and diversity analysis, we provide multifaceted evidence that bacterial communities in fact exhibit strong distribution patterns. This is driven by selection due to factors such as local soil characteristics. Altogether, these findings suggest that the processes underpinning diversity patterns are more unified across all domains of life than previously thought, which has broad implications for the understanding and management of soil biodiversity.

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The Abundance and Taxonomic Diversity of Filterable Forms of Bacteria during Succession in the Soils of Antarctica (Bunger Hills)

Microorganisms ◽

10.3390/microorganisms9081728 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1728

Author(s):

Alina G. Kudinova ◽

Andrey V. Dolgih ◽

Nikita S. Mergelov ◽

Ilya G. Shorkunov ◽

Olga A. Maslova ◽

...

Keyword(s):

Bacterial Communities ◽

Taxonomic Diversity ◽

Survival Strategies ◽

Rrna Gene ◽

Phylogenetic Groups ◽

Antarctic Soils ◽

Soil Bacterial Communities ◽

Dormant Forms ◽

Soil Bacterial ◽

New Research

Previous studies have shown that a significant part of the bacterial communities of Antarctic soils is represented by cells passing through filters with pore sizes of 0.2 µm. These results raised new research questions about the composition and diversity of the filterable forms of bacteria (FFB) in Antarctic soils and their role in the adaptation of bacteria to the extreme living conditions. To answer such questions, we analyzed the succession of bacterial communities during incubation of Antarctic soil samples from the Bunger Hills at increased humidity and positive temperatures (5°C and 20°C). We determined the total number of viable cells by fluorescence microscopy in all samples and assessed the taxonomic diversity of bacteria by next-generation sequencing of the 16S rRNA gene region. Our results have shown that at those checkpoints where the total number of cells reached the maximum, the FFB fraction reached its minimum, and vice versa. We did not observe significant changes in taxonomic diversity in the soil bacterial communities during succession. During our study, we found that the soil bacterial communities as a whole and the FFB fraction consist of almost the same phylogenetic groups. We suppose rapid transition of the cells of the active part of the bacterial population to small dormant forms is one of the survival strategies in extreme conditions and contributes to the stable functioning of microbial communities in Antarctic soils.

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Long-term agrichemical use leads to alterations in bacterial community diversity

Plant Soil and Environment ◽

10.17221/414/2012-pse ◽

2012 ◽

Vol 58 (No. 10) ◽

pp. 452-458 ◽

Cited By ~ 3

Author(s):

H. Tan ◽

M. Barret ◽

O. Rice ◽

D.N. Dowling ◽

J. Burke ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Spring Barley ◽

Community Diversity ◽

Rrna Gene ◽

Soil Bacterial Communities ◽

Culture Independent ◽

Concomitant Reduction ◽

Soil Bacterial

  Bacterial communities are key drivers of soil fertility and agriculture productivity. Understanding how soil bacterial communities change in response to different conditions is an important aspect in the development of sustainable agriculture. There is a desire to reduce the current reliance on high inputs of chemicals and fertilisers in agriculture, but limited data are available on how this might impact soil bacterial communities. This study investigated the bacterial communities in a spring barley monoculture site subjected to two different input regimes for over 12 years: a conventional chemical/fertiliser regime, and a reduced input regime. A culture independent approach was performed to compare the bacterial communities through 16S rRNA gene PCR-DGGE. PCO analysis revealed that the rhizosphere has a strong structuring effect on the bacterial community. Moreover, high inputs of agrichemicals lead to an increase of phosphorus level in the soil and a concomitant reduction of the bacterial diversity. These results may help to evaluate the environmental risks associated with agrichemical usage.  

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Resistance, Resilience, and Recovery of Dryland Soil Bacterial Communities Across Multiple Disturbances

Frontiers in Microbiology ◽

10.3389/fmicb.2021.648455 ◽

2021 ◽

Vol 12 ◽

Author(s):

Blaire Steven ◽

Michala L. Phillips ◽

Jayne Belnap ◽

La Verne Gallegos-Graves ◽

Cheryl R. Kuske ◽

...

Keyword(s):

Bacterial Communities ◽

Soil Structure ◽

Bacterial Biomass ◽

Natural Resistance ◽

Rrna Gene ◽

Community Recovery ◽

Soil Bacterial Communities ◽

Dryland Ecosystems ◽

Soil Bacterial ◽

And Function

Dryland ecosystems are sensitive to perturbations and generally slow to recover post disturbance. The microorganisms residing in dryland soils are especially important as they contribute to soil structure and nutrient cycling. Disturbance can have particularly strong effects on dryland soil structure and function, yet the natural resistance and recovery of the microbial components of dryland soils has not been well documented. In this study, the recovery of surface soil bacterial communities from multiple physical and environmental disturbances is assessed. Samples were collected from three field sites in the vicinity of Moab, UT, United States, 6 to 7 years after physical and climate disturbance manipulations had been terminated, allowing for the assessment of community recovery. Additionally, samples were collected in a transect that included three habitat patches: the canopy zone soils under the dominant shrubs, the interspace soils that are colonized by biological soil crusts, and edge soils at the plot borders. Field site and habitat patch were significant factors structuring the bacterial communities, illustrating that sites and habitats harbored unique soil microbiomes. Across the different sites and disturbance treatments, there was evidence of significant bacterial community recovery, as bacterial biomass and diversity were not significantly different than control plots. There was, however, a small number of 16S rRNA gene amplicon sequence variants that distinguished particular treatments, suggesting that legacy effects of the disturbances still remained. Taken together, these data suggest that dryland bacterial communities may possess a previously unappreciated potential to recover within years of the original disturbance.

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Impact of Rocky Desertification Control on Soil Bacterial Community in Karst Graben Basin, Southwestern China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.636405 ◽

2021 ◽

Vol 12 ◽

Author(s):

Qiang Li ◽

Ang Song ◽

Hui Yang ◽

Werner E. G. Müller

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Control Area ◽

Soil Bacterial Community ◽

Rrna Gene ◽

Natural Ecosystem ◽

Rocky Desertification ◽

Soil Bacterial Communities ◽

Edaphic Properties ◽

Soil Bacterial

Microorganisms play critical roles in belowground ecosystems, and karst rocky desertification (KRD) control affects edaphic properties and vegetation coverage. However, the relationship between KRD control and soil bacterial communities remains unclear. 16S rRNA gene next-generation sequencing was used to investigate soil bacterial community structure, composition, diversity, and co-occurrence network from five ecological types in KRD control area. Moreover, soil physical-chemical properties and soil stoichiometry characteristics of carbon, nitrogen and phosphorus were analyzed. Soil N and P co-limitation decreased in the contribution of the promotion of KRD control on edaphic properties. Though soil bacterial communities appeared strongly associated with soil pH, soil calcium, soil phosphorus and plant richness, the key factor to determine their compositions was the latter via changed edaphic properties. The co-occurrence network analysis indicated that soil bacterial network complexity in natural ecosystem was higher than that in additional management ecosystem. Candidatus Udaeobacter, Chthoniobacterales, and Pedosphaeraceae were recognized as the key taxa maintaining karst soil ecosystems in KRD control area. Our results indicate that natural recovery is the suitable way for restoration and rehabilitation of degraded ecosystems, and thus contribute to the ongoing endeavor to appraise the interactions among soil-plant ecological networks.

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