scholarly journals Micro-aggregation of a pristine grassland soil selects for bacterial and fungal communities and changes in nitrogen cycling potentials

2021 ◽  
Author(s):  
Christoph Keuschnig ◽  
Jean Martins ◽  
Aline Navel ◽  
Pascal Simonet ◽  
Catherine Larose
Keyword(s):  
Particle Size ◽  
Nitrogen Cycling ◽  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Microbial Interactions ◽  
Fungal Communities ◽  
Supernatant Fraction ◽  
Soil Microbial ◽  
Microbial Analysis

Microbial analysis at the micro scale of soil is essential to the overall understanding of microbial organization and interactions, and necessary for a better understanding of soil ecosystem functioning. While bacterial communities have been extensively described, little is known about the organization of fungal communities as well as functional potentials at scales relevant to microbial interactions. Fungal and bacterial communities and changes in nitrogen cycling potentials in the pristine Rothamsted Park Grass soil (bulk soil) as well as in its particle size sub-fractions (PSFs; > 250 µm, 250-63 µm, 63-20 µm, 20-2 µm, < 2 µm and supernatant) were studied. The potential for nitrogen reduction was found elevated in bigger aggregates. The relative abundance of Basidiomycota deceased with decreasing particle size, Ascomycota showed an increase and Mucoromycota became more prominent in particles less than 20 µm. Bacterial community structures changed below 20 µm at the scale where microbes operate.Strikingly, only members of two bacterial and one fungal phyla (Proteobacteria, Bacteroidota and Ascomycota, respectively) were washed-off the soil during fractionation and accumulated in the supernatant fraction where most of the detected bacterial genera (e.g., Pseudomonas, Massilia, Mucilaginibacter, Edaphobaculum, Duganella, Janthinobacterium and Variovorax) were previously associated with exopolysaccharide production and biofilm formation.Overall, the applied method shows potential to study soil microbial communities at micro scales which might be useful in studies focusing on the role of specific fungal taxa in soil structure formation as well as research on how and by whom biofilm-like structures are distributed and organized in soil.

LDPE microplastics affect soil microbial communities and nitrogen cycling

2021 ◽  
Vol 773 ◽  
pp. 145640
Author(s):  
Lili Rong ◽  
Longfei Zhao ◽  
Leicheng Zhao ◽  
Zhipeng Cheng ◽  
Yiming Yao ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Nitrogen Cycling ◽  
Soil Microbial Communities ◽  
Soil Microbial

scholarly journals Increased microbial expression of organic nitrogen cycling genes in long-term warmed grassland soils

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Joana Séneca ◽  
Andrea Söllinger ◽  
Craig W. Herbold ◽  
Petra Pjevac ◽  
Judith Prommer ◽  
...  
Keyword(s):  
Nitrogen Cycling ◽  
Cell Walls ◽  
Organic Nitrogen ◽  
Soil Microbial Communities ◽  
Microbial Cell ◽  
Ambient Conditions ◽  
Soil Microbial ◽  
Soil Temperatures ◽  
Microbial Turnover

AbstractGlobal warming increases soil temperatures and promotes faster growth and turnover of soil microbial communities. As microbial cell walls contain a high proportion of organic nitrogen, a higher turnover rate of microbes should also be reflected in an accelerated organic nitrogen cycling in soil. We used a metatranscriptomics and metagenomics approach to demonstrate that the relative transcription level of genes encoding enzymes involved in the extracellular depolymerization of high-molecular-weight organic nitrogen was higher in medium-term (8 years) and long-term (>50 years) warmed soils than in ambient soils. This was mainly driven by increased levels of transcripts coding for enzymes involved in the degradation of microbial cell walls and proteins. Additionally, higher transcription levels for chitin, nucleic acid, and peptidoglycan degrading enzymes were found in long-term warmed soils. We conclude that an acceleration in microbial turnover under warming is coupled to higher investments in N acquisition enzymes, particularly those involved in the breakdown and recycling of microbial residues, in comparison with ambient conditions.

scholarly journals Mixed-Cropping Between Field Pea Varieties Alters Root Bacterial and Fungal Communities

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Anthony Horner ◽  
Samuel S. Browett ◽  
Rachael E. Antwis
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Crop Production ◽  
Agricultural Soils ◽  
Critical Role ◽  
Agricultural Practices ◽  
Microbial Interactions ◽  
Field Pea ◽  
Fungal Communities ◽  
Mixed Cropping

AbstractModern agricultural practices have vastly increased crop production but negatively affected soil health. As such, there is a call to develop sustainable, ecologically-viable approaches to food production. Mixed-cropping of plant varieties can increase yields, although impacts on plant-associated microbial communities are unclear, despite their critical role in plant health and broader ecosystem function. We investigated how mixed-cropping between two field pea (Pisum sativum L.) varieties (Winfreda and Ambassador) influenced root-associated microbial communities and yield. The two varieties supported significantly different fungal and bacterial communities when grown as mono-crops. Mixed-cropping caused changes in microbial communities but with differences between varieties. Root bacterial communities of Winfreda remained stable in response to mixed-cropping, whereas those of Ambassador became more similar to Winfreda. Conversely, root fungal communities of Ambassador remained stable under mixed-cropping, and those of Winfreda shifted towards the composition of Ambassador. Microbial co-occurrence networks of both varieties were stronger and larger under mixed-cropping, which may improve stability and resilience in agricultural soils. Both varieties produced slightly higher yields under mixed-cropping, although overall Ambassador plants produced higher yields than Winfreda plants. Our results suggest that variety diversification may increase yield and promote microbial interactions.

The role of land management and elevation in shaping soil microbial communities: Insights from the Central European Alps

2020 ◽  
Vol 150 ◽  
pp. 107951
Author(s):  
Nadine Praeg ◽  
Julia Seeber ◽  
Georg Leitinger ◽  
Erich Tasser ◽  
Christian Newesely ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Land Management ◽  
Soil Microbial Communities ◽  
European Alps ◽  
Central European ◽  
Soil Microbial

scholarly journals Historical land use has long-term effects on microbial community assembly processes in forest soils

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Ernest D. Osburn ◽  
Frank O. Aylward ◽  
J. E. Barrett
Keyword(s):  
Land Use ◽  
Microbial Community ◽  
Community Assembly ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
Long Term Effects ◽  
Soil Microbial ◽  
Historical Land Use ◽  
Microbial Community Assembly

AbstractLand use change has long-term effects on the structure of soil microbial communities, but the specific community assembly processes underlying these effects have not been identified. To investigate effects of historical land use on microbial community assembly, we sampled soils from several currently forested watersheds representing different historical land management regimes (e.g., undisturbed reference, logged, converted to agriculture). We characterized bacterial and fungal communities using amplicon sequencing and used a null model approach to quantify the relative importance of selection, dispersal, and drift processes on bacterial and fungal community assembly. We found that bacterial communities were structured by both selection and neutral (i.e., dispersal and drift) processes, while fungal communities were structured primarily by neutral processes. For both bacterial and fungal communities, selection was more important in historically disturbed soils compared with adjacent undisturbed sites, while dispersal processes were more important in undisturbed soils. Variation partitioning identified the drivers of selection to be changes in vegetation communities and soil properties (i.e., soil N availability) that occur following forest disturbance. Overall, this study casts new light on the effects of historical land use on soil microbial communities by identifying specific environmental factors that drive changes in community assembly.

scholarly journals Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Kateryna Zhalnina ◽  
Karsten Zengler ◽  
Dianne Newman ◽  
Trent R. Northen
Keyword(s):  
Microbial Communities ◽  
Metabolic Networks ◽  
Soil Microbial Communities ◽  
Microbial Interactions ◽  
Microbial Consortia ◽  
Cellular Biology ◽  
Model Organisms ◽  
Soil Microbial ◽  
Integrative Framework ◽  
Genome Annotations

ABSTRACTThe chemistry underpinning microbial interactions provides an integrative framework for linking the activities of individual microbes, microbial communities, plants, and their environments. Currently, we know very little about the functions of genes and metabolites within these communities because genome annotations and functions are derived from the minority of microbes that have been propagated in the laboratory. Yet the diversity, complexity, inaccessibility, and irreproducibility of native microbial consortia limit our ability to interpret chemical signaling and map metabolic networks. In this perspective, we contend that standardized laboratory ecosystems are needed to dissect the chemistry of soil microbiomes. We argue that dissemination and application of standardized laboratory ecosystems will be transformative for the field, much like how model organisms have played critical roles in advancing biochemistry and molecular and cellular biology. Community consensus on fabricated ecosystems (“EcoFABs”) along with protocols and data standards will integrate efforts and enable rapid improvements in our understanding of the biochemical ecology of microbial communities.

scholarly journals Plant Biomass and Soil Nutrients Mainly Explain the Variation of Soil Microbial Communities during Secondary Succession on the Loess Plateau

2021 ◽  
Author(s):  
Miao-Ping Xu ◽  
Jia-Yi Wang ◽  
Xin-Hui Han ◽  
Cheng-Jie Ren ◽  
Gai-He Yang
Keyword(s):  
Microbial Biomass ◽  
Soil Nutrients ◽  
Soil Microbial Biomass ◽  
Plant Biomass ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
The Loess Plateau ◽  
Soil Microbial ◽  
Plant Characteristics ◽  
Soil Bacterial

Abstract Soil microorganisms play an important role in the circulation of materials and nutrients between plants and soil ecosystems, but the drivers of microbial community composition and diversity remain uncertain in different vegetation restoration patterns. We studied soil physicochemical properties (i.e., soil moisture, bulk density, pH, soil nutrients, available nutrients), plant characteristics (i.e., Shannon index [HPlant] and Richness index [SPlant], litter biomass [LB], and fine root biomass [FRB]), and microbial variables (biomass, enzyme activity, diversity and composition of bacterial and fungal communities) in different plant succession patterns (Robinia pseudoacacia [MF], Caragana korshinskii [SF] and grassland [GL]) on the Loess Plateau. The herb communities, soil microbial biomass and enzyme activities were strongly affected by vegetation restoration. And soil bacterial and fungal communities were significantly different from each other at the sites. Furthermore, LB and FRB were significantly positively correlated with SBacteria, soil microbial biomass, enzyme activities, Proteobacteria, Zygomycota and Cercozoa, while negatively correlated with Actinobacteria and Basidiomycota. In addition, soil water content (SW), pH and nutrients have important effects on the bacterial and fungal diversities, Acidobacteria, Proteobacteria, Nitrospirae, Zygomycota and microbial biomass. Furthermore, plant characteristics and soil properties modulated the composition and diversity of soil microorganisms, respectively. Overall, the relative contribution of vegetation and soil to the diversity and composition of soil bacterial and fungal communities illustrated that plant characteristics and soil properties may synergistically modulate soil microbial communities. And soil bacterial and fungal communities mainly depend on plant biomass and soil nutrients.

scholarly journals Activation of the SA-Associated Plant Defense Pathway Alters the Composition of Soil Bacterial Communities

2021 ◽  
Author(s):  
Jing Zhang ◽  
Peter G.L. Klinkhamer ◽  
Klaas Vrieling ◽  
T. Martijn Bezemer
Keyword(s):  
Plant Growth ◽  
Microbial Communities ◽  
Signaling Pathway ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Soil Microbial Communities ◽  
Core Microbiome ◽  
Soil Microbial ◽  
Soil Bacterial ◽  
Sa Signaling

Abstract Background and aimsMany plant species grow better in sterilized than in live soil. Foliar application of SA mitigates this negative effect of live soil on the growth of the plant Jacobaea vulgaris. To examine what causes the positive effect of SA application on plant growth in live soils, we analyzed the effects of SA application on the composition of active rhizosphere bacteria in the live soil. Methods We studied this over four consecutive plant cycles (generations), using mRNA sequencing of the microbial communities in the rhizosphere of J. vulgaris. ResultsOur study shows that the composition of the rhizosphere bacterial communities of J. vulgaris greatly differed among generations. Application of SA resulted in both increases and decreases in a number of active bacterial genera in the rhizosphere soil, but the genera that were affected by the treatment differed among generations. In the first generation, there were no genera that were significantly affected by the SA treatment, indicating that induction of the SA defense pathway in plants does not lead to immediate changes in the soil microbial community. 89 species out of the total 270 (32.4%) were present in all generations in all soils of SA-treated and control plants suggesting that these make up the “core” microbiome. On average in each generation, 72.9% of all genera were present in both soils. Application of SA to plants significantly up-regulated genera of Caballeronia, unclassified Cytophagaceae, Crinalium and Candidatus Thermofonsia Clade 2, and down-regulated genera of Thermomicrobiales, unclassified Rhodobacterales, Paracoccus and Flavihumibacter. While the functions of many of these bacteria are poorly understood, bacteria of the genus Caballeronia play an important role in fixing nitrogen and promoting plant growth, and hence this suggests that activation of the SA signaling pathway in J. vulgaris plants may select for bacterial genera that are beneficial to the plant. ConclusionsOverall, our study shows that aboveground activation of defenses in the plant affects soil microbial communities and, as soil microbes can greatly influence plant performance, this implies that induction of plant defenses can lead to complex above-belowground feedbacks. Further studies should examine how activation of the SA signaling pathway in the plant changes the functional genes of the rhizosphere soil bacterial community.

scholarly journals Tillage practices and residue management manipulate soil bacterial and fungal assembly and co-occurrence network patterns in maize agroecosystem

2020 ◽  
Author(s):  
Wei Yang ◽  
Yupeng Guan ◽  
Cheng Zhai ◽  
Lin Du ◽  
Yanxiang Wu ◽  
...  
Keyword(s):  
Soil Microbial Communities ◽  
Residue Management ◽  
Fungal Communities ◽  
No Tillage ◽  
Deep Tillage ◽  
Soil Microbial ◽  
Tillage Practices ◽  
Soil Bacterial ◽  
Network Patterns ◽  
Residue Retention

Abstract Background: Tillage practices and residue management are highly important agricultural practices. However, very few studies have examined the influence of tillage practices and residue management on both bacterial and fungal communities and network patterns in consecutive years. Results: We examined the effects of different tillage practices, including no tillage, rotary tillage, and deep tillage, on the soil bacterial and fungal communities and co-occurrence networks following residue removal and residue retention in 2017 and 2018. This study showed that both bacterial and fungal communities were unaffected by tillage practices in 2017, but they were significantly influenced in 2018. In addition, soil fungal operational taxonomic unit (OTU) richness was significantly enhanced by deep tillage compared with no tillage in 2018, while bacterial OTU richness was unaffected in either year. Tillage practices had differing effects on the soil microbial network patterns, with rotary and deep tillage increasing the complexity of bacterial networks but simplifying fungal networks. However, residue retention only induced a shift in the fungal community in 2018 without an obvious effect in the bacterial community in both years. In addition, residue retention simplified soil bacterial and fungal networks in 2018. Conclusions: This study highlighted the dissimilar responses of bacterial and fungal networks to tillage practices and emphasized that tillage practice is more important than residue management in shaping soil microbial communities.

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