Short-interval reburns in the boreal forest alter soil bacterial communities, reflecting increased pH and poor conifer seedling establishment

Increasing burn rates (percentage area burned annually) in some biomes are leading to fires burning in close succession, triggering rapid vegetation change as well as altering soil properties. Despite the importance of soil microbes for nutrient cycling and as plant symbionts, the effects of increased fire frequency on belowground microbial communities remain largely unknown. We present a study of the effects of short interval reburns (defined here as <20 years between fires) on soil bacterial communities in the boreal forest of northwestern Canada, using a paired site design that spans wetlands and uplands, with 50 sites total. We asked whether short interval reburns significantly alter soil bacterial community composition and richness, and which bacterial taxa are associated with greater or lower fire frequency. We found that, while short interval reburns had no significant effect on bacterial richness, there were significant changes in overall community composition. We did not find correlations between understory vegetation community dissimilarities and bacterial community dissimilarities, suggesting the primary drivers of changes induced by short interval reburns may differ between plants and microbes. We identified an abundant Blastococcus sp. that was consistently enriched in short interval reburns, in both wetlands and uplands, indicating its role as a strongly "pyrophilous" bacterium. We also identified an abundant Callaberonia sordidicola taxon as being consistently depleted in short interval reburns. This endophytic diazotrophic organism is a robust colonizer of pine and spruce seedlings and has the ability to increase seedling growth, due in part to large contributions of fixed nitrogen. Its depletion in short-interval reburn sites raises questions about whether this is contributing to - or merely reflects - poor conifer seedling recolonization post-fire at short-interval reburns.

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Quality of Irrigation Water Affects Soil Functionality and Bacterial Community Stability in Response to Heat Disturbance

Applied and Environmental Microbiology ◽

10.1128/aem.02087-17 ◽

2017 ◽

Vol 84 (4) ◽

Cited By ~ 5

Author(s):

Sammy Frenk ◽

Yitzhak Hadar ◽

Dror Minz

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Resource Availability ◽

Bacterial Communities ◽

Anthropogenic Activities ◽

Bacterial Community Composition ◽

Treated Wastewater ◽

Soil Bacterial Communities ◽

High Resource ◽

Soil Bacterial

ABSTRACTAnthropogenic activities alter the structure and function of a bacterial community. Furthermore, bacterial communities structured by the conditions the anthropogenic activities present may consequently reduce their stability in response to an unpredicted acute disturbance. The present mesocosm-scale study exposed soil bacterial communities to different irrigation water types, including freshwater, fertilized freshwater, treated wastewater, and artificial wastewater, and evaluated their response to a disturbance caused by heat. These effectors may be considered deterministic and stochastic forces common in agricultural operations of arid and semiarid regions. Bacterial communities under conditions of high mineral and organic carbon availability (artificial wastewater) differed from the native bacterial community and showed a proteobacterial dominance. These bacterial communities had a lower resistance to the heat treatment disturbance than soils under conditions of low resource availability (high-quality treated wastewater or freshwater). The latter soil bacterial communities showed a higher abundance of operational taxonomic units (OTUs) classified asBacilli. These results were elucidated by soil under conditions of high resource availability, which lost higher degrees of functional potential and had a greater bacterial community composition change. However, the functional resilience, after the disturbance ended, was higher under a condition of high resource availability despite the bacterial community composition shift and the decrease in species richness. The functional resilience was directly connected to the high growth rates of certainBacteroidetesand proteobacterial groups. A high stability was found in samples that supported the coexistence of both resistant OTUs and fast-growing OTUs.IMPORTANCEThis report presents the results of a study employing a hypothesis-based experimental approach to reveal the forces involved in determining the stability of a soil bacterial community to disturbance. The resultant postdisturbance bacterial community composition dynamics and functionality were analyzed. The paper demonstrates the relatedness of community structure and stability under cultivation conditions prevalent in an arid area under irrigation with water of different qualities. The use of common agricultural practices to demonstrate these features has not been described before. The combination of a fundamental theoretical issue in ecology with common and concerning disturbances caused by agricultural practice makes this study unique. Furthermore, the results of the present study have applicable importance regarding soil conservation, as it enables a better characterization and monitoring of stressed soil bacterial communities and possible intervention to reduce the stress. It will also be of valued interest in coming years, as fresh water scarcity and the use of alternative water sources are expected to rise globally.

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Pavement Overrides the Effects of Tree Species on Soil Bacterial Communities

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18042168 ◽

2021 ◽

Vol 18 (4) ◽

pp. 2168

Author(s):

Yinhong Hu ◽

Weiwei Yu ◽

Bowen Cui ◽

Yuanyuan Chen ◽

Hua Zheng ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Community Composition ◽

Tree Species ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Soil Bacterial Community ◽

Soil Bacterial Communities ◽

Pine Stands ◽

Soil Bacterial

Human disturbance and vegetation are known to affect soil microorganisms. However, the interacting effects of pavement and plant species on soil bacterial communities have received far less attention. In this study, we collected soil samples from pine (Pinus tabuliformis Carr.), ash (Fraxinus chinensis), and maple (Acer truncatum Bunge) stands that grew in impervious, pervious, and no pavement blocks to investigate the way pavement, tree species, and their interaction influence soil bacterial communities by modifying soil physicochemical properties. Soil bacterial community composition and diversity were evaluated by bacterial 16S amplicon sequencing. The results demonstrated that soil bacterial community composition and diversity did differ significantly across pavements, but not with tree species. The difference in soil bacterial community composition across pavements was greater in pine stands than ash and maple stands. Soil bacterial diversity and richness indices decreased beneath impervious pavement in pine stands, and only bacterial richness indices decreased markedly in ash stands, but neither showed a significant difference across pavements in maple stands. In addition, bacterial diversity did not differ dramatically between pervious pavement and no pavement soil. Taken together, these results suggest that pavement overwhelmed the effects of tree species on soil bacterial communities, and had a greater effect on soil bacterial communities in pine stands, followed by ash and maple stands. This study highlights the importance of anthropogenic disturbance, such as pavement, which affects soil microbial communities.

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Proximate grassland and shrub-encroached sites show dramatic restructuring of soil bacterial communities

PeerJ ◽

10.7717/peerj.7304 ◽

2019 ◽

Vol 7 ◽

pp. e7304

Author(s):

Xingjia Xiang ◽

Sean M. Gibbons ◽

He Li ◽

Haihua Shen ◽

Haiyan Chu

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Vegetation Type ◽

Bacterial Community Composition ◽

Shrub Encroachment ◽

Soil Bacterial Community ◽

Grassland Soils ◽

Soil Bacterial Communities ◽

Soil Bacterial

Background Changes in aboveground community composition and diversity following shrub encroachment have been studied extensively. Recently, shrub encroachment was associated with differences in belowground bacterial communities relative to non-encroached grassland sites hundreds of meters away. This spatial distance between grassland and shrub sites left open the question of how soil bacterial communities associated with different vegetation types might differ within the same plot location. Methods We examined soil bacterial communities between shrub-encroached and adjacent (one m apart) grassland soils in Chinese Inner Mongolian, using high-throughput sequencing method (Illumina, San Diego, CA, USA). Results Shrub-encroached sites were associated with dramatic restructuring of soil bacterial community composition and predicted metabolic function, with significant increase in bacterial alpha-diversity. Moreover, bacterial phylogenic structures showed clustering in both shrub-encroached and grassland soils, suggesting that each vegetation type was associated with a unique and defined bacterial community by niche filtering. Finally, soil organic carbon (SOC) was the primary driver varied with shifts in soil bacterial community composition. The encroachment was associated with elevated SOC, suggesting that shrub-mediated shifts in SOC might be responsible for changes in belowground bacterial community. Discussion This study demonstrated that shrub-encroached soils were associated with dramatic restructuring of bacterial communities, suggesting that belowground bacterial communities appear to be sensitive indicators of vegetation type. Our study indicates that the increased shrub-encroached intensity in Inner Mongolia will likely trigger large-scale disruptions in both aboveground plant and belowground bacterial communities across the region.

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From pine to pasture: land use history has long-term impacts on soil bacterial community composition and functional potential

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa041 ◽

2020 ◽

Vol 96 (4) ◽

Author(s):

Syrie M Hermans ◽

Matthew Taylor ◽

Gwen Grelet ◽

Fiona Curran-Cournane ◽

Hannah L Buckley ◽

...

Keyword(s):

Land Use ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Reference Sites ◽

Functional Potential ◽

Soil Bacterial Communities ◽

Soil Bacterial

ABSTRACT Bacterial communities are crucial to soil ecosystems and are known to be sensitive to environmental changes. However, our understanding of how present-day soil bacterial communities remain impacted by historic land uses is limited; implications for their functional potential are especially understudied. Through 16S rRNA gene amplicon and shotgun metagenomic sequencing, we characterized the structure and functional potential of soil bacterial communities after land use conversion. Sites converted from pine plantations to dairy pasture were sampled five- and eight-years post conversion. The bacterial community composition and functional potential at these sites were compared to long-term dairy pastures and pine forest reference sites. Bacterial community composition and functional potential at the converted sites differed significantly from those at reference sites (P = 0.001). On average, they were more similar to those in the long-term dairy sites and showed gradual convergence (P = 0.001). Differences in composition and functional potential were most strongly related to nutrients such as nitrogen, Olsen P and the carbon to nitrogen ratio. Genes related to the cycling of nitrogen, especially denitrification, were underrepresented in converted sites compared to long-term pasture soils. Together, our study highlights the long-lasting impacts land use conversion can have on microbial communities, and the implications for future soil health and functioning.

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Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

Applied and Environmental Microbiology ◽

10.1128/aem.00335-09 ◽

2009 ◽

Vol 75 (15) ◽

pp. 5111-5120 ◽

Cited By ~ 1989

Author(s):

Christian L. Lauber ◽

Micah Hamady ◽

Rob Knight ◽

Noah Fierer

Keyword(s):

Bacterial Community ◽

Soil Ph ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Spatial Scales ◽

Bacterial Community Composition ◽

Phylogenetic Structure ◽

Soil Bacterial Communities ◽

Soil Bacterial Community Structure ◽

Soil Bacterial

ABSTRACT Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R2 = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.

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Perennials but not slope aspect affect the diversity of soil bacterial communities in the northern Negev Desert, Israel

Soil Research ◽

10.1071/sr17010 ◽

2018 ◽

Vol 56 (2) ◽

pp. 123 ◽

Cited By ~ 1

Author(s):

Ahuva Vonshak ◽

Menachem Y. Sklarz ◽

Ann M. Hirsch ◽

Osnat Gillor

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Community Composition ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Plant Litter ◽

Negev Desert ◽

Slope Aspect ◽

Desert Shrubs ◽

Soil Bacterial

Underneath the canopy of perennials in arid regions, moderate soil temperature and evaporation, as well as plant litter create islands of higher fertility in the low-productivity landscape, known as ‘resource islands’. The sparse distribution of these resource islands is mirrored by soil microbial communities, which mediate a large number of biogeochemical transformations underneath the plants. We explored the link between the bacterial community composition and two prevalent desert shrubs, Zygophyllum dumosum and Artemisia herba-alba, on northern- and southern-facing slopes in the northern highlands of the Negev Desert (Israel), at the end of a drought winter mild rainy season. We sequenced the bacterial community and analysed the physicochemical properties of the soil under the shrub canopies and from barren soil in replicate slopes. The soil bacterial diversity was independent of slope aspect, but differed according to shrub presence or type. Links between soil bacterial community composition and their associated desert shrubs were found, enabling us to link bacterial diversity with shrub type or barren soils. Our results suggest that plants and their associated bacterial communities are connected to survival and persistence under the harsh desert conditions.

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Effects of shade stress on morphophysiology and rhizosphere soil bacterial communities of two contrasting shade-tolerant turfgrasses

10.21203/rs.2.10288/v1 ◽

2019 ◽

Author(s):

Juanjuan Fu ◽

Yilan Luo ◽

Pengyue Sun ◽

Jinzhu Gao ◽

Donghao Zhao ◽

...

Keyword(s):

Bacterial Community ◽

Plant Growth ◽

Bacterial Communities ◽

Shade Tolerance ◽

High Throughput Sequencing ◽

Rhizosphere Soil ◽

Bacterial Community Composition ◽

Soil Bacterial Communities ◽

Soil Bacterial ◽

The Impact

Abstract Background: Perturbations in the abiotic stress directly or indirectly affect plants and root-associated microbial communities. Shade stress presents one of the major abiotic limitations for turfgrass growth, as light availability is severely reduced under a leaf canopy. Studies have shown that shade stress influences plant growth and alters plant metabolism, yet little is known about how it affects the structure of rhizosphere soil bacterial communities. In this study, a glasshouse experiment was conducted to examine the impact of shade stress on the physiology of two contrasting shade-tolerant turfgrasses and their rhizosphere soil microbes. Shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrasss (Lolium perenne, LP) were used. Bacterial community composition was assayed using high-throughput sequencing. Results: Our physiochemical data showed that under shade stress, OJ maintained higher photosynthetic capacity and root growth, thus OJ was found to be more shade-tolerant than LP. Illumina sequencing data revealed that shade stress had little impact on the diversity of the OJ and LP’s bacterial communities, but instead impacted the composition of bacterial communities. The bacterial communities were mostly composed of Proteobacteria and Acidobacteria in OJ soil. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress, indicating that they are important drivers determining bacterial community structures. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. Conclusion: OJ was more shade-tolerant than LP. Shifts in rhizosphere soil bacterial community structure play a vital role in shade-tolerance of OJ plants.

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The Effects of Pavement Types on Soil Bacterial Communities across Different Depths

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph16101805 ◽

2019 ◽

Vol 16 (10) ◽

pp. 1805 ◽

Cited By ~ 1

Author(s):

Weiwei Yu ◽

Yinhong Hu ◽

Bowen Cui ◽

Yuanyuan Chen ◽

Xiaoke Wang

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Shannon Index ◽

Soil Bacterial Community ◽

Total Carbon ◽

Bacterial Composition ◽

Soil Bacterial ◽

Micro Organisms

Pavements have remarkable effects on topsoil micro-organisms, but it remains unclear how subsoil microbial communities respond to pavements. In this study, ash trees (Fraxinus Chinensis) were planted on pervious pavement (PP), impervious pavement (IPP), and non-pavement (NP) plots. After five years, we determined the soil bacterial community composition and diversity by high-throughput sequencing of the bacterial 16S rRNA gene. The results of our field experiment reveal that the presence of pavement changed soil bacterial community composition and decreased the Shannon index, but had no impact on the Chao 1 at the 0–20 cm layer. However, we achieved the opposite result at a depth of 20–80 cm. Furthermore, there was a significant difference in bacterial community composition using the Shannon index and the Chao 1 at the 80–100 cm layer. Soil total carbon (TC), total nitrogen (TN), available phosphorus (AP), NO3−-N, and available potassium (AK) were the main factors that influenced soil bacterial composition and diversity across different pavements. Soil bacterial composition and diversity had no notable difference between PP and IPPs at different soil layers. Our results strongly indicate that pavements have a greater impact on topsoil bacterial communities than do subsoils, and PPs did not provide a better habitat for micro-organisms when compared to IPPs in the short term.

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Soil pH and Organic Carbon Properties Drive Soil Bacterial Communities in Surface and Deep Layers Along an Elevational Gradient

Frontiers in Microbiology ◽

10.3389/fmicb.2021.646124 ◽

2021 ◽

Vol 12 ◽

Author(s):

Qiuxiang Tian ◽

Ying Jiang ◽

Yanan Tang ◽

Yu Wu ◽

Zhiyao Tang ◽

...

Keyword(s):

Community Composition ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Soil Layer ◽

Elevational Gradient ◽

Deep Soil ◽

Soil Layers ◽

Soil C ◽

Soil Bacterial Communities ◽

Soil Bacterial

Elevational gradients strongly affect the spatial distribution and structure of soil bacterial communities. However, our understanding of the effects and determining factors is still limited, especially in the deep soil layer. Here, we investigated the diversity and composition of soil bacterial communities in different soil layers along a 1,500-m elevational gradient in the Taibai Mountain. The variables associated with climate conditions, plant communities, and soil properties were analyzed to assess their contributions to the variations in bacterial communities. Soil bacterial richness and α-diversity showed a hump-shaped trend with elevation in both surface and deep layers. In the surface layer, pH was the main factor driving the elevational pattern in bacterial diversity, while in the deep layer, pH and soil carbon (C) availability were the two main predictors. Bacterial community composition differed significantly along the elevational gradient in all soil layers. In the surface layer, Acidobacteria, Delta-proteobacteria, and Planctomycetes were significantly more abundant in the lower elevation sites than in the higher elevation sites; and Gemmatimonadetes, Chloroflexi, and Beta-proteobacteria were more abundant in the higher elevation sites. In the deep layer, AD3 was most abundant in the highest elevation site. The elevational pattern of community composition co-varied with mean annual temperature, mean annual precipitation, diversity and basal area of trees, pH, soil C availability, and soil C fractions. Statistical results showed that pH was the main driver of the elevational pattern of the bacterial community composition in the surface soil layer, while soil C fractions contributed more to the variance of the bacterial composition in the deep soil layer. These results indicated that changes in soil bacterial communities along the elevational gradient were driven by soil properties in both surface and deep soil layers, which are critical for predicting ecosystem functions under future climate change scenarios.

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Soil Bacterial Community Diversity and Composition as Affected by Tillage Intensity Treatments in Corn-Soybean Production Systems

Microbiology Research ◽

10.3390/microbiolres12010012 ◽

2021 ◽

Vol 12 (1) ◽

pp. 157-172

Author(s):

Shankar G. Shanmugam ◽

Normie W. Buehring ◽

Jon D. Prevost ◽

William L. Kingery

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Community Composition ◽

Production System ◽

Soil Microbial Community ◽

Production Systems ◽

Bacterial Community Composition ◽

Soybean Production ◽

Soil Microbial ◽

Soil Bacterial

Our understanding on the effects of tillage intensity on the soil microbial community structure and composition in crop production systems are limited. This study evaluated the soil microbial community composition and diversity under different tillage management systems in an effort to identify management practices that effectively support sustainable agriculture. We report results from a three-year study to determine the effects on changes in soil microbial diversity and composition from four tillage intensity treatments and two residue management treatments in a corn-soybean production system using Illumina high-throughput sequencing of 16S rRNA genes. Soil samples were collected from tillage treatments at locations in the Southern Coastal Plain (Verona, Mississippi, USA) and Southern Mississippi River Alluvium (Stoneville, Mississippi, USA) for soil analysis and bacterial community characterization. Our results indicated that different tillage intensity treatments differentially changed the relative abundances of bacterial phyla. The Mantel test of correlations indicated that differences among bacterial community composition were significantly influenced by tillage regime (rM = 0.39, p ≤ 0.0001). Simpson’s reciprocal diversity index indicated greater bacterial diversity with reduction in tillage intensity for each year and study location. For both study sites, differences in tillage intensity had significant influence on the abundance of Proteobacteria. The shift in the soil bacterial community composition under different tillage systems was strongly correlated to changes in labile carbon pool in the system and how it affected the microbial metabolism. This study indicates that soil management through tillage intensity regime had a profound influence on diversity and composition of soil bacterial communities in a corn-soybean production system.

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