Long-term no-till: A major driver of fungal communities in dryland wheat cropping systems

Sharma‐Poudyal, Dipak; Schlatter, Daniel; Yin, Chuntao; Hulbert, Scot H.; Paulitz, T. C.

doi:10.1371/journal.pone.0184611

Cited by 66 publications

(43 citation statements)

References 56 publications

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“…Interestingly, microbial taxonomic 5 and functional 8 diversities in the same soil and treatments are in agreement with the results that we now report of abundance of hydrolases. Increases in fungal biomass in NT in comparison with the CT have been reported, 63 as well as differences in the strategies of C utilization, 64 and, in general, in our study, hydrolases sequences were attributed to fungi, Verticillium and Colletotrichum (lipases and laccases), and Aspergillus (proteases). Interestingly, for the amylases, sequences were attributed mainly to the archaea S. acidocaldarius ; important roles of mesophilic and thermophilic Group I archaea in soil, more specifically in N-cycling (ammonia oxidizers) have been recently described, 65 and now we extend their importance to the amylases.…”

Section: Discussionsupporting

confidence: 73%

Outstanding impact of soil tillage on the abundance of soil hydrolases revealed by a metagenomic approach

Souza

Cantão

Nogueira

et al. 2018

Brazilian Journal of Microbiology

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The soil represents the main source of novel biocatalysts and biomolecules of industrial relevance. We searched for hydrolases in silico in four shotgun metagenomes (4,079,223 sequences) obtained in a 13-year field trial carried out in southern Brazil, under the no-tillage (NT), or conventional tillage (CT) managements, with crop succession (CS, soybean/wheat), or crop rotation (CR, soybean/maize/wheat/lupine/oat). We identified 42,631 hydrolases belonging to five classes by comparing with the KEGG database, and 44,928 sequences by comparing with the NCBI-NR database. The abundance followed the order: lipases > laccases > cellulases > proteases > amylases > pectinases. Statistically significant differences were attributed to the tillage system, with the NT showing about five times more hydrolases than the CT system. The outstanding differences can be attributed to the management of crop residues, left on the soil surface in the NT, and mechanically broken and incorporated into the soil in the CT. Differences between the CS and the CR were slighter, 10% higher for the CS, but not statistically different. Most of the sequences belonged to fungi (Verticillium, and Colletotrichum for lipases and laccases, and Aspergillus for proteases), and to the archaea Sulfolobus acidocaldarius for amylases. Our results indicate that agricultural soils under conservative managements may represent a hotspot for bioprospection of hydrolases.

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Section: Discussionsupporting

confidence: 73%

Outstanding impact of soil tillage on the abundance of soil hydrolases revealed by a metagenomic approach

Souza

Cantão

Nogueira

et al. 2018

Brazilian Journal of Microbiology

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“…A number of studies have found that tillage reduces total fungal biomass in agricultural soils (Helgason et al, 2009(Helgason et al, , 2010Mathew et al, 2012;Cho et al, 2017). A comparison of no-till and standard till dryland wheat found the fungal community was dominated by Ascomycota in both systems, with Ascomycota and Basidiomycota showing significant changes in the tilled system (Sharma-Poudyal et al, 2017). We also observed Ascomycota as the dominant phylum in all treatments, but it was not responsive to tillage.…”

Section: Tillage Effectsmentioning

confidence: 51%

“…It has been proposed that fungal taxa selected by conventionally tilled systems are primary colonizers of mechanically damaged plant residues and produce large numbers of tillage-resistant conidia (Sharma-Poudyal et al, 2017). Taxa more abundant in no-till are either endophytes or other groups adapted to utilizing intact roots, or taxa with extensive hyphal networks that can be disrupted by tillage (Sharma-Poudyal et al, 2017). It may be that groups that do not fall into these categories are likely to remain unaffected by the tillage regime.…”

Section: Tillage Effectsmentioning

confidence: 99%

“…For example, AMF consistently experience reduction in numbers, root colonization rates and diversity with tillage (Helgason et al, 2010;Schnoor et al, 2011;Wetzel et al, 2014;Säle et al, 2015;Jesus et al, 2016). Far less is known about other groups of fungi such as the saproptrophs that make up 50-80% of the overall fungal community (Balser et al, 2005;Nguyen et al, 2016), although saprotrophs that colonize fresh, mature plant residues turned into the soil by tillage have been shown to increase under standard tillage (Sharma-Poudyal et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

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Cover cropping and no-till increase diversity and symbiotroph:saprotroph ratios of soil fungal communities

Schmidt

Mitchell

Scow

2019

Soil Biology and Biochemistry

200

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Fungi are important members of soil microbial communities in row-crop and grassland soils, provide essential ecosystem services such as nutrient cycling, organic matter decomposition, and soil structure, but fungi are also more sensitive to physical disturbance than other microorganisms. Adoption of conservation management practices such as no-till and cover cropping shape the structure and function of soil fungal communities. No-till eliminates or greatly reduces the physical disturbance that redistributes organisms and nutrients in the soil profile and disrupts fungal hyphal networks, while cover crops provide additional types and greater abundance of organic carbon sources. In a long-term, row crop field experiment in California's Central Valley we hypothesized that a more diverse and plant symbiont-enriched fungal soil community would develop in soil managed with reduced tillage practices and/or cover crops compared to standard tillage and no cover crops. We measured the interacting effects of tillage and cover cropping on fungal communities based on fungal ITS sequence assigned to ecological guilds. Functional groups within fungal communities were most sensitive to longterm tillage practices, with 45% of guild-assigned taxa responding to tillage, and a higher proportion of symbiotroph taxa under no-till. In contrast, diversity measures reflected greater sensitivity to cover crops, with higher phylogenetic diversity observed in soils managed with cover crops, though only 10% of guild-assigned taxa responded to cover crops. The relative abundance of pathotrophs did not vary across the management treatments. Cover cropping increased species diversity, while no-till shifted the symbiotroph:saprotroph ratio to favor symbiotrophs. These management-induced shifts in fungal community composition could lead to greater ecosystem resilience and provide greater access of crops to limiting resources.

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“…The two most prominent cellulolytic taxa in the consortium, Cellvibrio and Chaetomium, are commonly observed in studies of agroecosystems. Cellvibrio dominated access to cellulosic C in two previous SIP studies of agricultural soils [12,35] and both Cellvibrio and Chaetomium are favored by tillage [36][37][38][39].…”

Section: Discussionmentioning

confidence: 99%

Competitive exclusion and metabolic dependency among microorganisms structure the cellulose economy of agricultural soil

Wilhelm

Pepe-Ranney

Weisenhorn

et al. 2020

Preprint

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Background Microorganisms that degrade cellulose utilize extracellular processes that yield free intermediates which promote interactions with non-cellulolytic organisms. We hypothesized that these interactions determine the ecological and physiological traits governing the fate of cellulosic carbon (C) in soil. We used data from a metagenomic-SIP experiment to perform comparative genomics and characterize the attributes of cellulolytic and non-cellulolytic taxa accessing 13C from cellulose. We hypothesized that cellulolytic taxa would exhibit competitive traits to limit access, while non-cellulolytic taxa would display metabolic dependency, such as signatures of adaptive gene loss. We tested our hypotheses by evaluating genomic traits indicative of competitive exclusion or metabolic dependency, such as antibiotic production, growth rate, surface attachment, biomass degrading potential and auxotrophy.Results The most 13C-enriched taxa were cellulolytic Cellvibrio (Gammaproteobacteria) and Chaetomium (Ascomycota), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria, demonstrating differences in dependency among cellulose degraders. Non-cellulolytic taxa that accessed 13C from cellulose (Planctomycetales, Verrucomicrobia and Vampirovibrionales) were highly dependent, as indicated by patterns of auxotrophy and 13C-labeling (i.e. partial labelling or labeling at later-stages). Major 13C-labeled cellulolytic microbes (e.g. Sorangium, Actinomycetales, Rhizobiales and Caulobacteraceae) possessed adaptations for surface colonization (e.g. gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposition. Conclusions Our results demonstrate that access to cellulose was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion. These trade-offs influence microbial growth dynamics on particulate organic carbon and reveal that the fate of carbon is governed by a complex economy within the microbial community. We propose three ecological groups to describe participants in this economy: (i) independent primary degraders, (ii) integrated primary degraders and (iii) mutualists, opportunists and parasites. The relative importance and taxonomic composition of these groups reported here should be considered context dependent, likely reflecting disturbance and management practices common to agricultural soils.

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Long-term no-till: A major driver of fungal communities in dryland wheat cropping systems

Cited by 66 publications

References 56 publications

Outstanding impact of soil tillage on the abundance of soil hydrolases revealed by a metagenomic approach

Outstanding impact of soil tillage on the abundance of soil hydrolases revealed by a metagenomic approach

Cover cropping and no-till increase diversity and symbiotroph:saprotroph ratios of soil fungal communities

Competitive exclusion and metabolic dependency among microorganisms structure the cellulose economy of agricultural soil

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