Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories

2021 ◽  
Vol 97 (4) ◽  
Author(s):  
Doreen Babin ◽  
Loreen Sommermann ◽  
Soumitra Paul Chowdhury ◽  
Jan H Behr ◽  
Martin Sandmann ◽  
...  
Keyword(s):  
Growth Regulators ◽  
Stress Responses ◽  
Crop Production ◽  
Agricultural Management ◽  
Plant Performance ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soil Microbiota ◽  
Sustainable Crop Production

ABSTRACT A better understanding of factors shaping the rhizosphere microbiota is important for sustainable crop production. We hypothesized that the effect of agricultural management on the soil microbiota is reflected in the assemblage of the rhizosphere microbiota with implications for plant performance. We designed a growth chamber experiment growing the model plant lettuce under controlled conditions in soils of a long-term field experiment with contrasting histories of tillage (mouldboard plough vs cultivator tillage), fertilization intensity (intensive standard nitrogen (N) + pesticides/growth regulators vs extensive reduced N without fungicides/growth regulators), and last standing field crop (rapeseed vs winter wheat). High-throughput sequencing of bacterial and archaeal 16S rRNA genes and fungal ITS2 regions amplified from total community DNA showed that these factors shaped the soil and rhizosphere microbiota of lettuce, however, to different extents among the microbial domains. Pseudomonas and Olpidium were identified as major indicators for agricultural management in the rhizosphere of lettuce. Long-term extensive fertilization history of soils resulted in higher lettuce growth and increased expression of genes involved in plant stress responses compared to intensive fertilization. Our work adds to the increasing knowledge on how soil microbiota can be manipulated by agricultural management practices which could be harnessed for sustainable crop production.

Impacts of switching tillage to no-tillage and vice versa on soil structure, enzyme activities, and prokaryotic community profiles in Argentinean semi-arid soils

2021 ◽  
Author(s):  
L A Gabbarini ◽  
E Figuerola ◽  
J P Frene ◽  
N B Robledo ◽  
F M Ibarbalz ◽  
...  
Keyword(s):  
Community Structure ◽  
Soil Structure ◽  
Management Practices ◽  
Soil Health ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Prokaryotic Community ◽  
C Cycle

Abstract The effects of tillage on soil structure, physiology, and microbiota structure were studied in a long-term field experiment, with side-to-side plots, established to compare effects of conventional tillage (CT) vs. no-till (NT) agriculture. After 27 years, part of the field under CT was switched to NT and vice versa. Soil texture, soil enzymatic profiles, and the prokaryotic community structure (16S rRNA genes amplicon sequencing) were analysed at two soil depths (0–5, 5–10 cm) in samples taken 6, 18, and 30 months after switching tillage practices. Soil enzymatic activities were higher in NT than CT, and enzymatic profiles responded to the changes much earlier than the overall prokaryotic community structure. Beta diversity measurements of the prokaryotic community indicated that the levels of stratification observed in long-term NT soils were already recovered in the new NT soils thirty months after switching from CT to NT. Bacteria and Archaea OTUs, which responded to NT were associated with coarse soil fraction, SOC and C cycle enzymes while CT responders were related to fine soil fractions and S cycle enzymes. This study showed the potential of managing the soil prokaryotic community and soil health through changes in agricultural management practices.

scholarly journals The Response of the Soil Microbiota to Long-Term Mineral and Organic Nitrogen Fertilization is Stronger in the Bulk Soil than in the Rhizosphere

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 456 ◽  
Author(s):  
Massimiliano Cardinale ◽  
Stefan Ratering ◽  
Aitak Sadeghi ◽  
Sushil Pokhrel ◽  
Bernd Honermeier ◽  
...  
Keyword(s):  
N Fertilization ◽  
16S Rrna Genes ◽  
Bulk Soil ◽  
Rrna Genes ◽  
Soil Microbiome ◽  
Future Research ◽  
Arable Soils ◽  
Mineral N ◽  
Bacterial Microbiota

The effects of different agronomic practices, such as fertilization regimes, can be experimentally tested in long-term experiments (LTE). Here, we aimed to evaluate the effect of different nitrogen fertilizations on the bacterial microbiota in both rhizosphere and bulk soil of sugar beet, in the Giessen-LTE (Germany). Fertilization treatments included mineral-N, manure, mineral-N + manure and no N-amendment. Metabarcoding and co-occurrence analysis of 16S rRNA genes, qPCR of amoA, nirK, nirS, nosZ-I and nosZ-II genes and soil physico-chemical analyses were performed. The effect of the fertilization treatments was more evident in the bulk soil, involving 33.1% of the microbiota. Co-occurrence analysis showed a rhizosphere cluster, dominated by Proteobacteria, Actinobacteria and Verrucomicrobia (hub taxa: Betaproteobacteriales), and a bulk soil cluster, dominated by Acidobacteria, Gemmatominadetes and “Latescibacteria” (hub taxa: Acidobacteria). In the bulk soil, mineral N-fertilization reduced nirK, amoA, nosZ-I and nosZ-II genes. Thirteen Operational taxonomic units (OTUs) showed 23 negative correlations with gene relative abundances. These OTUs likely represent opportunistic species that profited from the amended mineral-N and outgrew the species carrying N-cycle genes. Our results indicate trajectories for future research on soil microbiome in LTE and add new experimental evidence that will be helpful for sustainable management of nitrogen fertilizations on arable soils.

scholarly journals Rhizosphere Bacterial Community Response to Continuous Cropping of Tibetan Barley

2020 ◽  
Vol 11 ◽  
Author(s):  
Youhua Yao ◽  
Xiaohua Yao ◽  
Likun An ◽  
Yixiong Bai ◽  
Deqing Xie ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Total Nitrogen ◽  
Rhizosphere Soil ◽  
Community Response ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Continuous Cropping ◽  
Health Maintenance ◽  
Rhizosphere Bacterial Community

Long-term continuous cropping influences the nutrient of soil and microbiome of the rhizosphere, resulting in the yield decrease of crops. Tibetan barley is a dominant cereal crop cultivated at high altitudes in Tibet. Its growth and yield are negatively affected by continuous cropping; however, the response of the rhizosphere microbial community to continuous cropping remains poorly understood. To address this question, we investigated the bacterial community structure and conducted predictive functional profiling on rhizosphere soil from Tibetan barley monocropped for 2–6 years. The results revealed that long-term continuous cropping markedly decreased total nitrogen and available nitrogen in rhizosphere soil. Illumina high-throughput sequencing of 16S rRNA genes indicated that the bacterial community was altered by continuous cropping; operational taxonomic units (OTUs), Shannon index, and Faith Phylogenetic Diversity decreased with increasing monocropping duration. Relative abundances of family Pseudomonadaceae, Cytophagaceae, and Nocardioidaceae were significantly increased, while those of Chitinophagaceae and Sphingomonadaceae were significantly decreased (all p < 0.05). Besides, continuous cropping significantly increased the abundance of bacteria associated with chemoheterotrophy, aromatic compound degradation, and nitrate reduction (p < 0.05). Generalized boosted regression model analysis indicated that total nitrogen was the most important contributor to the bacterial community diversity, indicating their roles in shaping the rhizosphere bacterial community during continuous cropping. Overall, continuous cropping had a significant impact on the structure of bacterial communities in rhizosphere soil of Tibetan barley, and these results will improve our understanding of soil bacterial community regulation and soil health maintenance in Tibetan barley farm systems.

Microbial community analysis of soils under different soybean cropping regimes in the Argentinean south-eastern Humid Pampas

2021 ◽  
Author(s):  
Gabriela Fernandez-Gnecco ◽  
Kornelia Smalla ◽  
Lorrie Maccario ◽  
Søren J Sørensen ◽  
Pablo Barbieri ◽  
...  
Keyword(s):  
Microbial Community ◽  
Cover Crops ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Temporal Shift ◽  
Soil Microbial ◽  
No Till

Abstract Soil microbial communities are key players of ecosystem processes and important for crop and soil health. The Humid Pampas region in Argentina concentrates 75% of the national soybean production, which is based on intensive use of agrochemicals, monocropping and no-till. A long-term field experiment under no-till management in the southeast of the Argentinean Pampas provides a unique opportunity to compare soybean under monocropping with cultivation including alternating cover crops or in a three-phase rotation. We hypothesized that cropping regimes and season affect soil microbial community composition and diversity. Amplicon sequencing of 16S rRNA genes and internal transcribed spacer fragments showed a stronger microbial seasonal dynamic in conservation regimes compared to monocropping. In addition, several bacterial (e.g. Catenulispora, Streptomyces and Bacillus) and fungal genera (e.g. Exophiala) with cropping regime-dependent differential relative abundances were identified. Despite a temporal shift in microbial and chemical parameters, this study shows that long-term cropping regimes shaped the soil microbiota. This might have important implications for soil quality and soybean performance and should therefore be considered in the development of sustainable agricultural managements.

scholarly journals Impact of Soil Drying-Rewetting Stress on Microbial Communities and Activities and on Degradation of Two Crop Protection Products

2004 ◽  
Vol 70 (5) ◽  
pp. 2577-2587 ◽  
Author(s):  
Manuel Pesaro ◽  
Gilles Nicollier ◽  
Josef Zeyer ◽  
Franco Widmer
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
Stress Responses ◽  
Crop Protection ◽  
16S Rrna Genes ◽  
Cell Counting ◽  
Rrna Genes ◽  
Soil Dna ◽  
Degradation Rates ◽  
The Impact

ABSTRACT Prior to registration of crop protection products (CPPs) their persistence in soil has to be determined under defined conditions. For this purpose, soils are collected in the field and stored for up to 3 months prior to the tests. During storage, stresses like drying may induce changes in microbiological soil characteristics (MSCs) and thus may influence CPP degradation rates. We investigated the influence of soil storage-related stress on the resistance and resilience of different MSCs by assessing the impact of a single severe drying-rewetting cycle and by monitoring recovery from this event for 34 days. The degradation and mineralization of the fungicide metalaxyl-M and the insecticide lufenuron were delayed by factors of 1.5 to 5.4 in the dried and rewetted soil compared to the degradation and mineralization in an undisturbed reference. The microbial biomass, as estimated by direct cell counting and from the soil DNA content, decreased on average by 51 and 24%, respectively. The bulk microbial activities, as determined by measuring substrate-induced respiration and fluorescein diacetate hydrolysis, increased after rewetting and recovered completely within 6 days after reequilibration. The effects on Bacteria, Archaea, and Pseudomonas were investigated by performing PCR amplification of 16S rRNA genes and reverse-transcribed 16S rRNA, followed by restriction fragment length polymorphism (RFLP) and terminal RFLP (T-RFLP) fingerprinting. Statistical analyses of RFLP and T-RFLP profiles indicated that specific groups in the microbial community were sensitive to the stress. In addition, evaluation of rRNA genes and rRNA as markers for monitoring the stress responses of microbial communities revealed overall similar sensitivities. We concluded that various structural and functional MSCs were not resistant to drying-rewetting stress and that resilience depended strongly on the parameter investigated.

scholarly journals Microbes as Biofertilizers, a Potential Approach for Sustainable Crop Production

2021 ◽  
Vol 13 (4) ◽  
pp. 1868
Author(s):  
Shaista Nosheen ◽  
Iqra Ajmal ◽  
Yuanda Song
Keyword(s):  
Crop Production ◽  
Cost Effective ◽  
Chemical Fertilizers ◽  
Promising Alternative ◽  
Sustainable Crop Production ◽  
Hazardous Chemical ◽  
Complex Forms ◽  
Global Food ◽  
Good Substitute

Continuous decline of earth’s natural resources and increased use of hazardous chemical fertilizers pose a great concern for the future of agriculture. Biofertilizers are a promising alternative to hazardous chemical fertilizers and are gaining importance for attaining sustainable agriculture. Biofertilizers play a key role in increasing crop yield and maintaining long-term soil fertility, which is essential for meeting global food demand. Microbes can interact with the crop plants and enhance their immunity, growth, and development. Nitrogen, phosphorous, potassium, zinc, and silica are the essential nutrients required for the proper growth of crops, but these nutrients are naturally present in insolubilized or complex forms. Certain microorganisms render them soluble and make them available to the plants. The potential microbes, their mode of action, along with their effect on crops, are discussed in this review. Biofertilizers, being cost effective, non-toxic, and eco-friendly, serve as a good substitute for expensive and harmful chemical fertilizers. The knowledge gained from this review can help us to understand the importance of microbes in agriculture and the ways to formulate these microbes as biofertilizers for sustainable crop production.

scholarly journals Humans differ in their personal microbial cloud

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1258 ◽  
Author(s):  
James F. Meadow ◽  
Adam E. Altrichter ◽  
Ashley C. Bateman ◽  
Jason Stenson ◽  
GZ Brown ◽  
...  
Keyword(s):  
16S Rrna ◽  
Indoor Air ◽  
Direct Contact ◽  
High Throughput Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Climate Chamber ◽  
Single Person ◽  
First Time

Dispersal of microbes between humans and the built environment can occur through direct contact with surfaces or through airborne release; the latter mechanism remains poorly understood. Humans emit upwards of 106biological particles per hour, and have long been known to transmit pathogens to other individuals and to indoor surfaces. However it has not previously been demonstrated that humans emit a detectible microbial cloud into surrounding indoor air, nor whether such clouds are sufficiently differentiated to allow the identification of individual occupants. We used high-throughput sequencing of 16S rRNA genes to characterize the airborne bacterial contribution of a single person sitting in a sanitized custom experimental climate chamber. We compared that to air sampled in an adjacent, identical, unoccupied chamber, as well as to supply and exhaust air sources. Additionally, we assessed microbial communities in settled particles surrounding each occupant, to investigate the potential long-term fate of airborne microbial emissions. Most occupants could be clearly detected by their airborne bacterial emissions, as well as their contribution to settled particles, within 1.5–4 h. Bacterial clouds from the occupants were statistically distinct, allowing the identification of some individual occupants. Our results confirm that an occupied space is microbially distinct from an unoccupied one, and demonstrate for the first time that individuals release their own personalized microbial cloud.

scholarly journals Resuscitation of soil microbiota after > 70-years of desiccation

2020 ◽  
Author(s):  
Jun Zhao ◽  
Dongfeng Chen ◽  
Wei Gao ◽  
Zhiying Guo ◽  
Zhongjun Jia ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Bacterial Abundance ◽  
Storage Conditions ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequencing Analysis ◽  
Osmotic Change ◽  
Abundance And Diversity ◽  
Strong Adaptation

AbstractThe abundance and diversity of bacteria in 24 historical soil samples under air-dried storage conditions for more than 70 years were assessed by quantification and high-throughput sequencing analysis of 16S rRNA genes. All soils contained a measurable abundance of bacteria varying from 103 to 108 per gram of soil and contrasting community compositions were observed in different background soils, suggesting that the bacteria detected were indigenous to the soil. Following a 4-week soil rewetting event, the bacterial abundance significantly increased in soils, indicating strong adaptation of soil bacteria to extreme osmotic change and high resuscitation potential of some bacteria over long periods of desiccation. Paenibacillus, Cohnella and two unclassified Bacillales genera within the phylum Firmicutes represented the most ubiquitously active taxa, which showed growth in the highest number of soils (≥12 soils), while genera Tumebacillus, Alicyclobacillus and Brevibacillus in the phylum Firmicutes displayed the highest growth rates in soils (with >1000-fold average increase) following rewetting. Additionally, some Actinobacteria and Proteobacteria genera showed relatively high activity following rewetting, suggesting that the resilience to long-term desiccation and rewetting is a common trait across phylogenetically divergent microbes. The present study thus demonstrated that diversified groups of microbes are present and potentially active in historically desiccated soils, which might be of importance in the context of microbial ecology.

scholarly journals Short and long-term effects of a synbiotic on clinical signs, the fecal microbiome, and metabolomic profiles in healthy research cats receiving clindamycin: a randomized, controlled trial

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5130 ◽  
Author(s):  
Jacqueline C. Whittemore ◽  
Jennifer E. Stokes ◽  
Nicole L. Laia ◽  
Joshua M. Price ◽  
Jan S. Suchodolski
Keyword(s):  
Randomized Controlled Trial ◽  
Controlled Trial ◽  
Clinical Signs ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Fecal Microbiome ◽  
Treatment Groups ◽  
Randomized Controlled ◽  
Short And Long Term

Background Antibiotic-associated gastrointestinal signs (AAGS) occur commonly in cats. Co-administration of synbiotics is associated with decreased AAGS in people, potentially due to stabilization of the fecal microbiome and metabolome. The purpose of this double-blinded randomized-controlled trial was to compare AAGS and the fecal microbiome and metabolome between healthy cats that received clindamycin with a placebo or synbiotic. Methods 16 healthy domestic shorthair cats from a research colony were randomized to receive 150 mg clindamycin with either a placebo (eight cats) or commercially-available synbiotic (eight cats) once daily for 21 days with reevaluation 603 days thereafter. All cats ate the same diet. Food consumption, vomiting, and fecal score were recorded. Fecal samples were collected daily on the last three days of baseline (days 5–7), treatment (26–28), and recovery (631–633). Sequencing of 16S rRNA genes and gas chromatography time-of-flight mass spectrometry was performed. Clinical signs, alpha and beta diversity metrics, dysbiosis indices, proportions of bacteria groups, and metabolite profiles were compared between treatment groups using repeated measures ANOVAs. Fecal metabolite pathway analysis was performed. P < 0.05 was considered significant. The Benjamini & Hochberg’s False Discovery Rate was used to adjust for multiple comparisons. Results Median age was six and five years, respectively, for cats in the placebo and synbiotic groups. Hyporexia, vomiting, diarrhea, or some combination therein were induced in all cats. Though vomiting was less in cats receiving a synbiotic, the difference was not statistically significant. Bacterial diversity decreased significantly on days 26–28 in both treatment groups. Decreases in Actinobacteria (Bifidobacterium, Collinsella, Slackia), Bacteriodetes (Bacteroides), Lachnospiraceae (Blautia, Coprococcus, Roseburia), Ruminococcaceae (Faecilobacterium, Ruminococcus), and Erysipelotrichaceae (Bulleidia, [Eubacterium]) and increases in Clostridiaceae (Clostridium) and Proteobacteria (Aeromonadales, Enterobacteriaceae) occurred in both treatment groups, with incomplete normalization by days 631–633. Derangements in short-chain fatty acid, bile acid, indole, sphingolipid, benzoic acid, cinnaminic acid, and polyamine profiles also occurred, some of which persisted through the terminal sampling timepoint and differed between treatment groups. Discussion Cats administered clindamycin commonly develop AAGS, as well as short- and long-term dysbiosis and alterations in fecal metabolites. Despite a lack of differences in clinical signs between treatment groups, significant differences in their fecal metabolomic profiles were identified. Further investigation is warranted to determine whether antibiotic-induced dysbiosis is associated with an increased risk of future AAGS or metabolic diseases in cats and whether synbiotic administration ameliorates this risk.

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