The chosen few—variations in common and rare soil bacteria across biomes

AbstractSoil bacterial communities are dominated by a few abundant species, while their richness is associated with rare species with largely unknown ecological roles and biogeography. Analyses of previously published soil bacterial community data using a novel classification of common and rare bacteria indicate that only 0.4% of bacterial species can be considered common and are prevalent across biomes. The remaining bacterial species designated as rare are endemic with low relative abundances. Observations coupled with mechanistic models highlight the central role of soil wetness in shaping bacterial rarity. An individual-based model reveals systematic shifts in community composition induced by low carbon inputs in drier soils that deprive common species of exhibiting physiological advantages relative to other species. We find that only a “chosen few” common species shape bacterial communities across biomes; however, their contributions are curtailed in resource-limited environments where a larger number of rare species constitutes the soil microbiome.

The role of ecosystem engineers in shaping the diversity and function of arid soil bacterial communities

10.1101/2020.12.15.422998 ◽

2020 ◽

Author(s):

Capucine Baubin ◽

Arielle M. Farrell ◽

Adam Šťovíček ◽

Lusine Ghazaryan ◽

Itamar Giladi ◽

...

Keyword(s):

Bacterial Communities ◽

Soil Samples ◽

Ecosystem Engineers ◽

Soil Microbiome ◽

Desert Ecosystems ◽

Arid Soil ◽

Ant Nests ◽

Soil Bacterial ◽

And Function

ABSTRACTEcosystem engineers (EEs) are present in every environment and are known to strongly influence ecological processes and thus shape the distribution of species and resources. In this study, we assessed the direct and indirect effect of two EEs (perennial shrubs and ant nests), individually and combined, on the composition and function of arid soil bacterial communities. To that end, top soil samples were collected in the Negev Desert Highlands during the dry season from four patch types: (1) barren soil; (2) under shrubs; (3) near ant nests; or (4) near ant nests situated under shrubs. The bacterial composition was evaluated in the soil samples (fourteen replicates per patch type) using 16S rRNA gene amplicon sequencing, together with physico-chemical measures of the soil, and the potential functions of the community. We have found that the EEs differently affected the community composition. Indeed, barren patches supported a soil microbiome, dominated by Rubrobacter and Proteobacteria, while in EE patches the Deinococcus-Thermus phylum was dominating. The presence of the EEs similarly enhanced the abundance of phototrophic, nitrogen cycle and stress- related genes. In addition, only when both EEs were combined, were the soil characteristics altered. Our results imply that arid landscapes foster unique communities selected by each EE(s), solo or in combination, yet these communities have similar potential biological traits to persist under the harsh arid conditions. Environments with multiple EEs are complicated to study due to the possibility of non-additive effects of EEs and thus further research should be done.IMPORTANCEEcosystem engineers are organisms that can create, modify, or maintain their habitat. They are present in various environments but are particularly conspicuous in desert ecosystems, where their presence is tightly linked to vital resources like water or nutrients. Despite their key role in structuring and controlling desert ecosystems, joint engineering, and their effect on soil function, are unknown. Our study explores the contributions of key ecosystem engineers to the diversity and function of their soil microbiome allowing better understanding of their role in shaping habitats and engineering their activity

Long-term nutrient enrichment of an oligotroph-dominated wetland increases bacterial diversity in bulk soils and plant rhizospheres

10.1101/2020.01.08.899781 ◽

2020 ◽

Author(s):

Regina B. Bledsoe ◽

Carol Goodwillie ◽

Ariane L. Peralta

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Community Composition ◽

Nutrient Enrichment ◽

Bacterial Communities ◽

Nutrient Addition ◽

Soil Microbiome ◽

The Core ◽

ABSTRACTIn nutrient-limited conditions, plants rely on rhizosphere microbial members to facilitate nutrient acquisition, and in return plants provide carbon resources to these root-associated microorganisms. However, atmospheric nutrient deposition can affect plant-microbe relationships by changing soil bacterial composition and by reducing cooperation between microbial taxa and plants. To examine how long-term nutrient addition shapes rhizosphere community composition, we compared traits associated with bacterial (fast growing copiotrophs, slow growing oligotrophs) and plant (C3 forb, C4 grass) communities residing in a nutrient poor wetland ecosystem. Results revealed that oligotrophic taxa dominated soil bacterial communities and that fertilization increased the presence of oligotrophs in bulk and rhizosphere communities. Additionally, bacterial species diversity was greatest in fertilized soils, particularly in bulk soils. Nutrient enrichment (fertilized vs. unfertilized) and plant association (bulk vs. rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass vs. forb) was similar within treatments but differed between fertilization treatments. The core forb microbiome consisted of 602 unique taxa, and the core grass microbiome consisted of 372 unique taxa. Forb rhizospheres were enriched in potentially disease suppressive bacterial taxa and grass rhizospheres were enriched in bacterial taxa associated with complex carbon decomposition. Results from this study demonstrate that fertilization serves as a strong environmental filter on the soil microbiome, which leads to distinct rhizosphere communities and can shift plant effects on the rhizosphere microbiome. These taxonomic shifts within plant rhizospheres could have implications for plant health and ecosystem functions associated with carbon and nitrogen cycling.ImportanceOver the last century, humans have substantially altered nitrogen and phosphorus cycling. Use of synthetic fertilizer and burning of fossil fuels and biomass have increased nitrogen and phosphorous deposition, which results in unintended fertilization of historically low-nutrient ecosystems. With increased nutrient availability, plant biodiversity is expected to decline and bacterial communities are anticipated to increase in abundance of copiotrophic taxa. Here, we address how bacterial communities associated with different plant functional types (forb, grass) shift due to long-term nutrient enrichment. Unlike other studies, results revealed an increase in bacterial diversity, particularly, of oligotrophic bacteria in fertilized plots. We observed that nutrient addition strongly determines forb and grass rhizosphere composition, which could indicate different metabolic preferences in the bacterial communities. This study highlights how long-term fertilization of oligotroph-dominated wetlands could alter the metabolism of rhizosphere bacterial communities in unexpected ways.

The effects of afforestation on soil bacterial communities in temperate grassland are modulated by soil chemical properties

PeerJ ◽

10.7717/peerj.6147 ◽

2019 ◽

Vol 7 ◽

pp. e6147 ◽

Cited By ~ 1

Author(s):

Shu-Hong Wu ◽

Bing-Hong Huang ◽

Jian Gao ◽

Siqi Wang ◽

Pei-Chun Liao

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Chemical Properties ◽

Soil Chemical Properties ◽

Soil Microbiome ◽

Apparent Lack ◽

Soil P ◽

Abundant Otus ◽

Grassland afforestation dramatically affects the abiotic, biotic, and ecological function properties of the original ecosystems. Interference from afforestation might disrupt the stasis of soil physicochemical properties and the dynamic balance of microbiota. Some studies have suggested low sensitivity of soil properties and bacterial community to afforestation, but the apparent lack of a significant relationship is probably due to the confounding effects of the generalist habitat and rare bacterial communities. In this study, soil chemical and prokaryotic properties in a 30-year-old Mongolia pine (Pinus sylvestris var. mongolica Litv.) afforested region and adjacent grassland in Inner Mongolia were classified and quantified. Our results indicate that the high richness of rare microbes accounts for the alpha-diversity of the soil microbiome. Few OTUs of generalist (core bacteria) and habitat-specialist bacteria are present. However, the high abundance of this small number of OTUs governs the beta-diversity of the grassland and afforested land bacterial communities. Afforestation has changed the soil chemical properties, thus indirectly affecting the soil bacterial composition rather than richness. The contents of soil P, Ca2+, and Fe3+ account for differentially abundant OTUs such as Planctomycetes and subsequent changes in the ecologically functional potential of soil bacterial communities due to grassland afforestation. We conclude that grassland afforestation has changed the chemical properties and composition of the soil and ecological functions of the soil bacterial community and that these effects of afforestation on the microbiome have been modulated by changes in soil chemical properties.

Duration of continuous cropping with straw return affects the composition and structure of soil bacterial communities in cotton fields

Canadian Journal of Microbiology ◽

10.1139/cjm-2017-0443 ◽

2018 ◽

Vol 64 (3) ◽

pp. 167-181 ◽

Cited By ~ 8

Author(s):

Lei Yang ◽

Lanlan Tan ◽

Fenghua Zhang ◽

William Jeffrey Gale ◽

Zhibo Cheng ◽

...

Keyword(s):

Bacterial Communities ◽

Bacterial Species ◽

Illumina Miseq ◽

Continuous Cropping ◽

Cotton Production ◽

Positive Effects ◽

Composition And Structure ◽

Straw Return ◽

Salinized land in the China’s Xinjiang Region is being reclaimed for continuous cotton production. The specific objectives of this field study were (i) to compare bacterial composition and diversity in unfarmed (i.e., unreclaimed) and continuously (5, 10, 15, and 20 years) cropped soils and (ii) to explore correlations between soil properties and the bacterial communities identified by Illumina MiSeq sequencing. The results showed that bacterial species richness and diversity increased for 10–15 years and then declined when salinized land was reclaimed for cotton production. Proteobacteria and Firmicutes were the dominant phyla in unfarmed soil. Continuous cropping reduced the abundance of Firmicutes but increased that of Chloroflexi, Acidobacteria, and Actinobacteria. Cluster analyses showed that the greatest similarities in bacterial communities were between the 5- and 10-year treatments and between the 15- and 20-year treatments. Soil pH, electrical conductivity, alkali-hydrolyzable N, and available P were significantly correlated with bacterial community distribution. Overall, cotton production improved soil physicochemical properties and altered the structure and composition of soil bacterial communities compared with unfarmed soil. These positive effects began to decrease after 10–15 years of continuous cotton production.

Impact of high carbon amendments and pre-crops on soil bacterial communities

Biology and Fertility of Soils ◽

10.1007/s00374-020-01526-0 ◽

2020 ◽

Vol 57 (2) ◽

pp. 305-317

Author(s):

Catherine W. Kamau ◽

Richard van Duijnen ◽

Christoph A. O. Schmid ◽

Helga E. Balàzs ◽

Julien Roy ◽

...

Keyword(s):

Wheat Straw ◽

Bacterial Diversity ◽

Bacterial Communities ◽

Spring Barley ◽

Winter Barley ◽

Soil Microbiome ◽

Molecular Barcoding ◽

C Stocks ◽

AbstractA 2-year outdoor mesocosm experiment was carried out to determine the effects of high C amendments (HCAs; wheat straw and sawdust) compared to a control with no addition of HCAs (no-HCA) and 2 different crop rotation systems (spring barley/winter barley and faba bean/winter barley) on soil bacterial communities using a molecular barcoding approach. Samples were analyzed after pre-crop harvest (T1) and harvest of winter barley (T2). Our data demonstrate a clear drop in bacterial diversity after winter barley harvest in the no-HCA and wheat straw treatment compared to the pre-crops. Sawdust application had a stabilizing effect on bacterial diversity compared to the pre-crops and induced an increase in carbon (C) stocks in soil which were however negatively correlated with yields. Main responders in the no-HCA and wheat straw treatment compared to the pre-crops were bacteria of the phyla Actinobacteria and Bacteroidetes which were enriched and bacteria belonging to Firmicutes, Gemmatimonadetes, Proteobacteria, and Gemmatimonadaceae which were depleted. Overall differences between wheat straw–amended and no-HCA control samples were small and included single ASVs from various phyla. In sawdust-amended samples, only a shift of some Proteobacteria families was observed compared to the no-HCA control. Overall, pre-crop plant species had small influence on the observed response pattern of the soil microbiome towards the amendments and was only visible for wheat straw.

Rapid Shifts in Bacterial Community Assembly under Static and Dynamic Hydration Conditions in Porous Media

Applied and Environmental Microbiology ◽

10.1128/aem.02057-19 ◽

2019 ◽

Vol 86 (1) ◽

Cited By ~ 1

Author(s):

Hannah Kleyer ◽

Robin Tecon ◽

Dani Or

Keyword(s):

Bacterial Community ◽

Aqueous Phase ◽

Community Assembly ◽

Bacterial Communities ◽

Critical Role ◽

Abundant Species ◽

Special Focus ◽

ABSTRACT The complexity of natural soils presents a challenge to the systematic identification and disentanglement of governing processes that shape natural bacterial communities. Studies have highlighted the critical role of the soil aqueous phase in shaping interactions among soil bacterial communities. To quantify and improve the attributability of soil aqueous-phase effects, we introduced a synthetic and traceable bacterial community to simple porous microcosms and subjected the community to constant or dynamic hydration conditions. The results were expressed in terms of absolute abundance and show species-specific responses to hydration and nutrient conditions. Hydration dynamics exerted a significant influence on the fraction of less-abundant species, especially after extended incubation periods. Phylogenetic relationships did not explain the group of most abundant species. The ability to quantify species-level dynamics in a bacterial community offers an important step toward deciphering the links between community composition and functions in dynamic terrestrial environments. IMPORTANCE The composition and activity of soil bacteria are central to various ecosystem services and soil biogeochemical cycles. A key factor for soil bacterial activity is soil hydration, which is in a constant state of change due to rainfall, drainage, plant water uptake, and evaporation. These dynamic changes in soil hydration state affect the structure and function of soil bacterial communities in complex ways often unobservable in natural soil. We designed an experimental system that retains the salient features of hydrated soil yet enables systematic evaluation of changes in a representative bacterial community in response to cycles of wetting and drying. The study shows that hydration cycles affect community abundance, yet most changes in composition occur with the less-abundant species (while the successful ones remain dominant). This research offers a new path for an improved understanding of bacterial community assembly in natural environments, including bacterial growth, maintenance, and death, with a special focus on the role of hydrological factors.

Insights Into the Diversity of Terrestrial Soil Bacterial Communities Associated With Four Contrasting Köppen Climatic Zones.

10.21203/rs.3.rs-524809/v1 ◽

2021 ◽

Author(s):

Girish R Nair ◽

Suresh S.S. Raja

Keyword(s):

Bacterial Communities ◽

High Throughput Sequencing ◽

Bacterial Species ◽

Community Diversity ◽

Climatic Zone ◽

Mean Annual Precipitation ◽

Mean Annual Temperature ◽

Climatic Zones ◽

Abstract Background: The multidirectional relationship between soil, its microbiota, and climate is crucial in modulating the bacterial community diversity and its survival in the terrestrial ecosystem. Therefore, it is imperative to understand the dynamics of soil bacterial communities thriving in geographical areas of varied climatic exposure. Results: The diversity of terrestrial soil bacterial communities thriving in four contrasting Köppen climatic zones of India was investigated for the first time using high-throughput sequencing. The results revealed that the bacterial species diversity, evenness and richness were highest in HSCZ (humid subtropical climatic zone). Firmicutes was the most abundant phylum in TWCZ (tropical wet climatic zone), ACZ (arid climatic zone), and HSCZ (humid subtropical climatic zone) while Proteobacteria in MCZ (Mountain climatic zone). The predominance of class Alphaproteobacteria, Actinobacteria with genera Bradyrhizobium, Chthoniobacter, and Mycobacterium, was observed in MCZ in contrast to class Bacilli with genera Bacillus and Paenibacillus in the rest of the zones. Correlation analysis showed that H’ (Shannon diversity) index, S (species richness), OTU abundance were positively correlated with moisture, TOC, K, MAP (mean annual precipitation) and negatively correlated with pH, Ca, N, B. Fe, P, Mg and MAT (mean annual temperature). Conclusion: This work mapped the occurrence and distribution of terrestrial soil bacterial communities in contrasting climatic zones that enabled us to assess the effect of climate in mentioned Köppen climatic zones on a taxonomic scale.

Phylogenetic dependence of plant-soil feedback promotes rare species in a subtropical forest

10.22541/au.163254879.90485546/v1 ◽

2021 ◽

Author(s):

Yuan Jiang ◽

Zihui Wang ◽

Chengjin Chu ◽

Steve Kembel ◽

Fangliang He

Keyword(s):

Rare Species ◽

Abundant Species ◽

Common Species ◽

Subtropical Forest ◽

Plant Soil ◽

Soil Feedback ◽

Local Abundance ◽

Phylogenetic Conservatism ◽

Test Soil ◽

Close Relatives

The widespread observation that rare species have stronger conspecific plant-soil feedback (PSF) than common species raises more questions than answers on how rare species can possibly win the dance with abundant species. Here, we test soil feedback effect of phylogenetically related species on seedlings of contrasting local abundance in a subtropical forest. The results showed that although rare species suffered strong negative PSF in soils of conspecifics or phylogenetically close relatives, no such feedback was found in the soils of distant relatives. In contrast, although common species had weak conspecific PSF, they suffered consistently strong heterospecific soil feedback. These mechanisms ensure that rare species would fare well in the neighborhood of phylogenetically distant heterospecifics but do poorly under their close relatives, while common species perform relatively well in their own neighborhood but poorly in others’. This phylogenetic conservatism in PSF facilitates the persistence of rare species in a community.