scholarly journals Soil bacterial biodiversity is driven by long-term pasture management, poultry litter, and cattle manure inputs

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7839 ◽  
Author(s):  
Yichao Yang ◽  
Amanda J. Ashworth ◽  
Jennifer M. DeBruyn ◽  
Cammy Willett ◽  
Lisa M. Durso ◽  
...  
Keyword(s):  
Poultry Litter ◽  
Soil Health ◽  
Soil Microbial Communities ◽  
Cattle Manure ◽  
Soil Microbiome ◽  
Pasture Management ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
The Impact

Soil microorganisms are important for maintaining soil health, decomposing organic matter, and recycling nutrients in pasture systems. However, the impact of long-term conservation pasture management on soil microbial communities remains unclear. Therefore, soil microbiome responses to conservation pasture management is an important component of soil health, especially in the largest agricultural land-use in the US. The aim of this study was to identify soil microbiome community differences following 13-years of pasture management (hayed (no cattle), continuously grazed, rotationally grazed with a fenced, un-grazed and unfertilized buffer strip, and a control (no poultry litter or cattle manure inputs)). Since 2004, all pastures (excluding the control) received annual poultry litter at a rate of 5.6 Mg ha−1. Soil samples were collected at a 0–15 cm depth from 2016–2017 either pre or post poultry litter applications, and bacterial communities were characterized using Illumina 16S rRNA gene amplicon sequencing. Overall, pasture management influenced soil microbial community structure, and effects were different by year (P < 0.05). Soils receiving no poultry litter or cattle manure had the lowest richness (Chao). Continuously grazed systems had greater (P < 0.05) soil community richness, which corresponded with greater soil pH and nutrients. Consequently, continuously grazed systems may increase soil diversity, owing to continuous nutrient-rich manure deposition; however, this management strategy may adversely affect aboveground plant communities and water quality. These results suggest conservation pasture management (e.g., rotationally grazed systems) may not improve microbial diversity, albeit, buffer strips were reduced nutrients and bacterial movement as evident by low diversity and fertility in these areas compared to areas with manure or poultry litter inputs. Overall, animal inputs (litter or manure) increased soil microbiome diversity and may be a mechanism for improved soil health.

scholarly journals Soil Microbial Community Structure and Physicochemical Properties in Amomum tsaoko-based Agroforestry Systems in the Gaoligong Mountains, Southwest China

2019 ◽  
Vol 11 (2) ◽  
pp. 546 ◽  
Author(s):  
Guizhou Liu ◽  
Man Jin ◽  
Chuantao Cai ◽  
Chaonan Ma ◽  
Zhongsuzhi Chen ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Biomass ◽  
Physicochemical Properties ◽  
Phospholipid Fatty Acid ◽  
Soil Microbial Communities ◽  
Total Carbon ◽  
Native Forest ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
The Impact

Amomum tsaoko is cultivated in forests of tropical and subtropical regions of China, and the planting area is expanding gradually. However, little attention has been paid to the impact of A. tsaoko cultivation on the soil characteristics of the regions. We analyzed the effects of the A. tsaoko-forest agroforestry system (AFs) on the composition of soil microbial communities with increasing stand ages. We also compared the soil physicochemical properties, microbial biomass, and phospholipid fatty acid (PLFA) composition between native forest (NF) and AFs. The results showed that the level of total carbon, nitrogen, and organic matter dramatically dropped in AFs with increasing stand ages. pH affected other soil properties and showed close correlation to total carbon (P = 0.0057), total nitrogen (P = 0.0146), organic matter (P = 0.0075), hydrolyzable nitrogen (P = 0.0085), available phosphorus (P < 0.0001), and available potassium (P = 0.0031). PLFAs of bacteria (F = 4.650, P = 0.037), gram-positive bacteria (F = 6.640, P = 0.015), anaerobe (F = 5.672, P = 0.022), and total PLFA (F = 4.349, P = 0.043) were significantly affected by different treatments, with the greatest value for NF treatment, and least value for AF5. However, the microbial biomass declined during the initial 5 years of cultivation, but it reached the previous level after more than 10 years of cultivation. Our research suggests that AFs is a profitable land-use practice in the Gaoligong Mountains and that AFs showed a recovering trend of the soil nutrient condition with increasing stand ages. However, the severe loss of nitrogen in the soil of AFs requires additional nitrogen during cultivation to restore it to pre-cultivation levels.

scholarly journals Effects of Long-term Cotton Continuous Cropping on Soil Microbiome

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hui Xi ◽  
Jili Shen ◽  
Zheng Qu ◽  
Dingyi Yang ◽  
Shiming Liu ◽  
...  
Keyword(s):  
Severe Disease ◽  
Soil Microbial Communities ◽  
Alpha Diversity ◽  
Taxonomic Composition ◽  
Soil Microbiome ◽  
Continuous Cropping ◽  
Bacterial Phyla ◽  
Soil Microbial ◽  
Microbial Groups

AbstractVerticillium wilt is a severe disease of cotton crops in Xinjiang and affecting yields and quality, due to the continuous cotton cropping in the past decades. The relationship between continuous cropping and the changes induced on soil microbiome remains unclear to date. In this study, the culture types of 15 isolates from Bole (5F), Kuitun (7F), and Shihezi (8F) of north Xinjiang were sclerotium type. Only isolates from field 5F belonged to nondefoliating pathotype, the others belonged to defoliating pathotype. The isolates showed pathogenicity differentiation in cotton. Fungal and bacterial communities in soils had some difference in alpha-diversity, relative abundance, structure and taxonomic composition, but microbial groups showed similarity in the same habitat, despite different sampling sites. The fungal phyla Ascomycota, and the bacterial phyla Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Gemmatimonadetes were strongly enriched. Verticillium abundance was significantly and positively correlated with AN, but negatively correlated with soil OM, AK and pH. Moreover, Verticillium was correlated in abundances with 5 fungal and 6 bacterial genera. Overall, we demonstrate that soil microbiome communities have similar responses to long-term continuous cotton cropping, providing new insights into the effects of continuous cotton cropping on soil microbial communities.

A single application of fertiliser or manure to a cropping field has limited long-term effects on soil microbial communities

Soil Research ◽  
2019 ◽  
Vol 57 (3) ◽  
pp. 228
Author(s):  
C. Celestina ◽  
P. W. G. Sale ◽  
J. R. Hunt ◽  
C. Tang ◽  
A. E. Franks
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Soil Microbial Community ◽  
Poultry Litter ◽  
Fungal Communities ◽  
Single Application ◽  
Long Term Effects ◽  
Soil Microbial Community Structure ◽  
Soil Microbial

A large-scale field experiment was used to investigate the long-term effects of a single application of manure or inorganic fertiliser on microbial communities in the topsoil and subsoil of a cropping field in south-west Victoria. Poultry litter (20 t ha–1) and fertiliser (with equivalent total nutrients to the manure) was either surface broadcast or deep ripped into the subsoil before sowing in 2014. Soil samples were collected from the 0–10 and 25–40cm horizons in each treatment immediately after harvest of the third successive crop in January 2017. Next-generation sequencing of the 16S and ITS rRNA genes was used to characterise the bacterial and fungal communities in the soil. Amendment type and method of placement had a limited effect on soil microbial community structure and diversity, three years after treatments were applied. Fungal communities exhibited weak responses to the poultry litter and fertiliser in comparison to a nil control, but none of the treatments had any detectable effect on bacterial communities. Differences in structure and diversity of microbial communities were overwhelmingly due to their vertical distribution in the soil profile, and not the application of different amendments to the soil by deep ripping or surface broadcasting. The strength and timing of the soil disturbance, plant selection effects and farm management history likely contributed to the lack of measurable response in the soil microbial community.

Bio-Organic Fertilizers Manipulate Abundance Patterns of Rhizosphere Soil Microbial Community Structure To Improve Tomato Productivity

2021 ◽  
Author(s):  
Bintao Li ◽  
Luodi Guo ◽  
Haoming Wang ◽  
Yulong Li ◽  
Hangxian Lai ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Microbial Communities ◽  
Crop Yields ◽  
Organic Fertilizer ◽  
Soil Microbial Communities ◽  
Organic Fertilizers ◽  
Soil Microbiome ◽  
Growth Stages ◽  
Soil Microbial Community Structure ◽  
Soil Microbial

Abstract Background Bio-organic fertilizers has been shown to improve crop yields, partially because of the effects on the structure and function in resident soil microbiome. Purpose and methods Whereas, it is unknown if such improvements have been facilitated by the particular action of microbial inoculants, or the compost substrate. To understand the ecological mechanisms to increase crop productivity by bio-organic fertilizers, we conducted a pot experiment tracking soil physicochemical factors and extracellular enzyme activity over two growth stages and variations of soil microbial communities caused by fertilization practices as below: Bacillus subtilis CY1 inoculation, swine compost, and bio-organic fertilizer. Results Results showed that different fertilization measures, especially bio-organic fertilizers, increased soil nutrients, enzyme activity, and the diversity of microbial communities. For quantifying the “effect size” of microbiota manipulation, we discoverd that, respectively, 19.94% and 48.99% of variation in the bacterial and fungal communities could be interpreted using tested fertilization practices. Fertilization-sensitive microbes showed taxonomy diversity and gave responses as guilds of taxa to specific treatments. The microbes exhibited medium to high degree of co-occurrence in the network and could be recruited, directly or indirectly, by B. subtilis CY1, suggesting that bio-organic fertilizer may allow manipulation of influential community members.Conclusion Together we demonstrated that the increase in tomato productivity by bio-organic fertilizer was caused by the synergistic effect of organic fertilizer and beneficial microorganisms, thus providing novel insights into the soil microbiome manipulation strategies of biologically-enhanced organic fertilizers.

scholarly journals Selection, Succession, and Stabilization of Soil Microbial Consortia

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Elias K. Zegeye ◽  
Colin J. Brislawn ◽  
Yuliya Farris ◽  
Sarah J. Fansler ◽  
Kirsten S. Hofmockel ◽  
...  
Keyword(s):  
Species Richness ◽  
Microbial Communities ◽  
Liquid Medium ◽  
Physical Environment ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
Liquid Media ◽  
Soil Matrix ◽  
Soil Microbial

ABSTRACTSoil microorganisms play fundamental roles in cycling of soil carbon, nitrogen, and other nutrients, yet we have a poor understanding of how soil microbiomes are shaped by their nutritional and physical environment. In this study, we investigated the successional dynamics of a soil microbiome during 21 weeks of enrichment on chitin and its monomer,N-acetylglucosamine. We examined succession of the soil communities in a physically heterogeneous soil matrix as well as a homogeneous liquid medium. The guiding hypothesis was that the initial species richness would influence the tendency for the selected consortia to stabilize and maintain a relatively constant community structure over time. We also hypothesized that long-term, substrate-driven growth would result in consortia with reduced species richness compared to the parent microbiome and that this process would be deterministic with relatively little variation between replicates. We found that the initial species richness does influence the long-term community stability in both liquid media and soil and that lower initial richness results in a more rapid convergence to stability. Despite use of the same soil inoculum and access to the same major substrate, the resulting community composition differed greatly in soil from that in liquid medium. Hence, distinct selective pressures in soils relative to homogenous liquid media exist and can control community succession dynamics. This difference is likely related to the fact that soil microbiomes are more likely to thrive, with fewer compositional changes, in a soil matrix than in liquid environments.IMPORTANCEThe soil microbiome carries out important ecosystem functions, but interactions between soil microbial communities have been difficult to study due to the high microbial diversity and complexity of the soil habitat. In this study, we successfully obtained stable consortia with reduced complexity that contained species found in the original source soil. These consortia and the methods used to obtain them can be a valuable resource for exploration of specific mechanisms underlying soil microbial community ecology. The results of this study also provide new experimental context to better inform how soil microbial communities are shaped by new environments and how a combination of initial taxonomic structure and physical environment influences stability.

scholarly journals Antimicrobial resistant gene prevalence in soils due to animal manure deposition and long-term pasture management

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10258
Author(s):  
Yichao Yang ◽  
Amanda J. Ashworth ◽  
Jennifer M. DeBruyn ◽  
Lisa M. Durso ◽  
Mary Savin ◽  
...  
Keyword(s):  
Best Management Practices ◽  
Management Practices ◽  
Poultry Litter ◽  
Animal Manure ◽  
The United States ◽  
Cattle Manure ◽  
Pasture Management ◽  
Grassland Soils ◽  
Best Management

The persistence of antimicrobial resistant (AMR) genes in the soil-environment is a concern, yet practices that mitigate AMR are poorly understood, especially in grasslands. Animal manures are widely deposited on grasslands, which are the largest agricultural land-use in the United States. These nutrient-rich manures may contain AMR genes. The aim of this study was to enumerate AMR genes in grassland soils following 14-years of poultry litter and cattle manure deposition and evaluate if best management practices (rotationally grazed with a riparian (RBR) area and a fenced riparian buffer strip (RBS), which excluded cattle grazing and poultry litter applications) relative to standard pasture management (continuously grazed (CG) and hayed (H)) minimize the presence and amount of AMR genes. Quantitative PCR (Q-PCR) was performed to enumerate four AMR genes (ermB, sulI, intlI, and blactx-m-32) in soil, cattle manure, and poultry litter environments. Six soil samples were additionally subjected to metagenomic sequencing and resistance genes were identified from assembled sequences. Following 14-years of continuous management, ermB, sulI, and intlI genes in soil were greatest (P < 0.05) in samples collected under long-term continuous grazing (relative to conservation best management practices), under suggesting overgrazing and continuous cattle manure deposition may increase AMR gene presence. In general, AMR gene prevalence increased downslope, suggesting potential lateral movement and accumulation based on landscape position. Poultry litter had lower abundance of AMR genes (ermB, sulI, and intlI) relative to cattle manure. Long-term applications of poultry litter increased the abundance of sulI and intlI genes in soil (P < 0.05). Similarly, metagenomic shotgun sequencing revealed a greater total number of AMR genes under long-term CG, while fewer AMR genes were found in H (no cattle manure) and RBS (no animal manure or poultry litter). Results indicate long-term conservation pasture management practices (e.g., RBS and RBR) and select animal manure (poultry litter inputs) may minimize the presence and abundance of AMR genes in grassland soils.

scholarly journals SOILomics; where Microbiome Genetics meets Precision Agriculture

2021 ◽  
Vol 26 (1) ◽  
pp. e943
Author(s):  
Dimitrios Vlachakis ◽  
Aspasia Efthimiadou
Keyword(s):  
Climate Change ◽  
Precision Agriculture ◽  
Management Practices ◽  
Soil Health ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
New Techniques ◽  
New Era ◽  
Soil Microbial ◽  
Soil Biochemistry

Advances in genetics, soil biochemistry and microbiome analysis are opening up a new era in Precision Agriculture. In this direction, new techniques bring groundbreaking changes in land management practices through direct or indirect management of soil microbial communities. There is huge demand for the protection and enhancement of soil health and climate change resilience of crops. The increase in population, food consumption and fast approaching climate change pose a new threat to mankind that only by being proactive and highly prepared to deploy all novel and innovative stratagems in state-of-the-art soil microbiome precision agriculture can be avoided.

scholarly journals Selection, succession and stabilization of soil microbial consortia

2019 ◽  
Author(s):  
Elias K. Zegeye ◽  
Colin J. Brislawn ◽  
Yuliya Farris ◽  
Sarah J. Fansler ◽  
Kirsten S. Hofmockel ◽  
...  
Keyword(s):  
Species Richness ◽  
Microbial Communities ◽  
Liquid Medium ◽  
Physical Environment ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
Liquid Media ◽  
Soil Matrix ◽  
Soil Microbial

ABSTRACTSoil microorganisms play fundamental roles in cycling of soil carbon, nitrogen and other nutrients, yet we have a poor understanding of how soil microbiomes are shaped by their nutritional and physical environment. Here we investigated the successional dynamics of a soil microbiome during 21-weeks of enrichment on chitin and its monomer,N-acetylglucosamine. We examined succession of the soil communities in a physically heterogeneous soil matrix as well as a highly mixed liquid medium. The guiding hypothesis was that the initial species richness would influence the tendency for the selected consortia to stabilize and maintain relatively constant community structure over time. We also hypothesized that long term, substrate-driven growth would result in consortia with reduced species richness as compared to the parent microbiome and that this process would be deterministic with relatively little variation between replicates. We found that the initial species richness does influence the long-term community stability in both liquid media and soil and that lower initial richness results in a more rapid convergence to stability. Despite use of the same soil inoculum and access to the same major substrate, the resulting community composition differed greatly in soil compared to liquid medium. Hence, distinct selective pressures in soils relative to homogenous liquid media exist and can control community succession dynamics. This difference is likely related to the fact that soil microbiomes are more likely to thrive, with fewer compositional changes, in a soil matrix compared to liquid environments.IMPORTANCEThe soil microbiome carries out important ecosystem functions, but interactions between soil microbial communities have been difficult to study due to the high microbial diversity and complexity of the soil habitat. Here we successfully obtained stable consortia with reduced complexity that contained species found in the original source soil. These consortia and the methods used to obtain them can be a valuable resource for exploration of specific mechanisms underlying soil microbial community ecology. The results of this study also provide new experimental context to better inform how soil microbial communities are shaped by new environments and how a combination of initial taxonomic structure and physical environment influences stability.

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