scholarly journals Core Microbiota in Agricultural Soils and Their Potential Associations with Nutrient Cycling

mSystems ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Shuo Jiao ◽  
Yiqin Xu ◽  
Jie Zhang ◽  
Xin Hao ◽  
Yahai Lu
Keyword(s):  
Nutrient Cycling ◽  
Microbial Ecology ◽  
Eastern China ◽  
Habitat Preferences ◽  
Soil Nutrient ◽  
Rice Soils ◽  
Core Microbiota ◽  
Continental Scale ◽  
The Core ◽  
Ecological Roles

ABSTRACT Revealing the ecological roles of the core microbiota in community maintaining and soil nutrient cycling is crucial for understanding ecosystem function, yet there is a dearth of continental-scale studies on this fundamental topic in microbial ecology. Here, we collected 251 soil samples from adjacent pairs of maize and rice fields at a continental scale in eastern China. We revealed the major ecological roles of the core microbiota in maintaining complex connections between bacterial taxa and their associations with belowground multinutrient cycling. By identifying the habitat preferences of the core microbiota, we built a continental atlas for mapping the spatial distributions of bacteria in agro-soils, which helps forecast the responses of agricultural ecosystems to anthropogenic disturbance. The multinutrient cycling index for maize and rice soils was related to bacterial α-diversity and β-diversity, respectively. Rice soils exhibited higher bacterial diversity and closer bacterial cooccurrence relationships than maize soils. In contrast to the macro- or microecological latitudinal richness patterns in natural terrestrial ecosystems, the bacteria in maize soils showed higher richness at high latitudes; however, this trend was not observed in rice soils. This study provides a new perspective on the distinct bacterial biogeographic patterns to predict the ecological roles of the core microbiota in agro-soils and thus helps manage soil bacterial communities for better provisioning of key ecosystem services. IMPORTANCE Disentangling the roles of the core microbiota in community maintaining and soil nutrient cycling is an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the spatial atlas and ecological roles of the core microbiota. A systematic, continental-scale survey was conducted using agro-soils in adjacent pairs of maize (dryland) and rice (wetland) fields across eastern China. The results indicate that the core microbiota play major ecological roles in maintaining complex connections between bacterial taxa and are associated with belowground multinutrient cycling. A continental atlas was built for mapping the bacterial spatial distributions in agro-soils through identifying their habitat preferences. This study represents a significant advance in forecasting the responses of agricultural ecosystems to anthropogenic disturbance and thus helps manage soil bacterial communities for better provisioning of key ecosystem services—the ultimate goal of microbial ecology.

Defining and quantifying the core microbiome: Challenges and prospects

2021 ◽  
Vol 118 (51) ◽  
pp. e2104429118
Author(s):  
Alexander T. Neu ◽  
Eric E. Allen ◽  
Kaustuv Roy
Keyword(s):  
Microbial Ecology ◽  
Representative Sample ◽  
Sequence Variants ◽  
Core Microbiome ◽  
The Core ◽  
Taxonomic Level ◽  
Functional Attributes ◽  
Wide Range ◽  
Ecological Roles ◽  
History Of

The term “core microbiome” has become widely used in microbial ecology over the last decade. Broadly, the core microbiome refers to any set of microbial taxa, or the genomic and functional attributes associated with those taxa, that are characteristic of a host or environment of interest. Most commonly, core microbiomes are measured as the microbial taxa shared among two or more samples from a particular host or environment. Despite the popularity of this term and its growing use, there is little consensus about how a core microbiome should be quantified in practice. Here, we present a brief history of the core microbiome concept and use a representative sample of the literature to review the different metrics commonly used for quantifying the core. Empirical analyses have used a wide range of metrics for quantifying the core microbiome, including arbitrary occurrence and abundance cutoff values, with the focal taxonomic level of the core ranging from phyla to amplicon sequence variants. However, many of these metrics are susceptible to sampling and other biases. Developing a standardized set of metrics for quantifying the core that accounts for such biases is necessary for testing specific hypotheses about the functional and ecological roles of core microbiomes.

scholarly journals Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China

mSystems ◽  
2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Bin Ma ◽  
Zhongmin Dai ◽  
Haizhen Wang ◽  
Melissa Dsouza ◽  
Xingmei Liu ◽  
...  
Keyword(s):  
Eastern China ◽  
Soil Microbial Communities ◽  
Natural Forest ◽  
Community Diversity ◽  
Biogeographic Patterns ◽  
Soil Microbial ◽  
Continental Scale ◽  
Forest Sites ◽  
Vegetation Gradient ◽  
Bacteria And Fungi

ABSTRACT Understanding biogeographic patterns is a precursor to improving our knowledge of the function of microbiomes and to predicting ecosystem responses to environmental change. Using natural forest soil samples from 110 locations, this study is one of the largest attempts to comprehensively understand the different patterns of soil archaeal, bacterial, and fungal biogeography at the continental scale in eastern China. These patterns in natural forest sites could ascertain reliable soil microbial biogeographic patterns by eliminating anthropogenic influences. This information provides guidelines for monitoring the belowground ecosystem’s decline and restoration. Meanwhile, the deviations in the soil microbial communities from corresponding natural forest states indicate the extent of degradation of the soil ecosystem. Moreover, given the association between vegetation type and the microbial community, this information could be used to predict the long-term response of the underground ecosystem to the vegetation distribution caused by global climate change. The natural forest ecosystem in Eastern China, from tropical forest to boreal forest, has declined due to cropland development during the last 300 years, yet little is known about the historical biogeographic patterns and driving processes for the major domains of microorganisms along this continental-scale natural vegetation gradient. We predicted the biogeographic patterns of soil archaeal, bacterial, and fungal communities across 110 natural forest sites along a transect across four vegetation zones in Eastern China. The distance decay relationships demonstrated the distinct biogeographic patterns of archaeal, bacterial, and fungal communities. While historical processes mainly influenced bacterial community variations, spatially autocorrelated environmental variables mainly influenced the fungal community. Archaea did not display a distance decay pattern along the vegetation gradient. Bacterial community diversity and structure were correlated with the ratio of acid oxalate-soluble Fe to free Fe oxides (Feo/Fed ratio). Fungal community diversity and structure were influenced by dissolved organic carbon (DOC) and free aluminum (Ald), respectively. The role of these environmental variables was confirmed by the correlations between dominant operational taxonomic units (OTUs) and edaphic variables. However, most of the dominant OTUs were not correlated with the major driving variables for the entire communities. These results demonstrate that soil archaea, bacteria, and fungi have different biogeographic patterns and driving processes along this continental-scale natural vegetation gradient, implying different community assembly mechanisms and ecological functions for archaea, bacteria, and fungi in soil ecosystems. IMPORTANCE Understanding biogeographic patterns is a precursor to improving our knowledge of the function of microbiomes and to predicting ecosystem responses to environmental change. Using natural forest soil samples from 110 locations, this study is one of the largest attempts to comprehensively understand the different patterns of soil archaeal, bacterial, and fungal biogeography at the continental scale in eastern China. These patterns in natural forest sites could ascertain reliable soil microbial biogeographic patterns by eliminating anthropogenic influences. This information provides guidelines for monitoring the belowground ecosystem’s decline and restoration. Meanwhile, the deviations in the soil microbial communities from corresponding natural forest states indicate the extent of degradation of the soil ecosystem. Moreover, given the association between vegetation type and the microbial community, this information could be used to predict the long-term response of the underground ecosystem to the vegetation distribution caused by global climate change. Author Video: An author video summary of this article is available.

Further Notes on Structural Types and Earth Movements

1931 ◽  
Vol 68 (1) ◽  
pp. 15-24
Author(s):  
J. S. Lee
Keyword(s):  
South Africa ◽  
North America ◽  
Critical Points ◽  
Eastern China ◽  
Point Of View ◽  
Continental Scale ◽  
Structural Types ◽  
Tectonic Features ◽  
Geological Magazine

In a previous paper published in the Geological Magazine, the writer made an attempt to discuss the mechanism of earth movement on a continental scale purely from a tectonic point of view. The problem is so vast and involved that some of the vital points were hardly touched upon, partly because of lack of space and partly of literature. The arrival of the admirable works of Dr. A. du Toit and Dr. E. Krenkel has enabled the writer to deduce the mechanism of the movements of South Africa directly from its tectonic features, which process is thought to be far more reliable than the type of argument used in the previous case although the results arrived at are essentially the same. The earlier movements in North America are now seen to furnish evidence of the same type of mechanism as that which staged the later movements. An epsilon type of structure has been recognized in Eastern China, which was then described as a mere arc. The problem of the distribution of concealed coalfields in England was in the previous paper barely touched upon. It is now proposed to consider some of the critical points bearing on the problem.

scholarly journals Assessing the strength and sensitivity of the core microbiota approach on a highly diverse sponge reef

2020 ◽  
Vol 22 (9) ◽  
pp. 3985-3999
Author(s):  
Carmen Astudillo‐García ◽  
James J. Bell ◽  
Jose M. Montoya ◽  
Lucas Moitinho‐Silva ◽  
Torsten Thomas ◽  
...  
Keyword(s):  
Core Microbiota ◽  
The Core ◽  
Sponge Reef

Using molecular microbial ecology to define differential responses to the inoculation of barley silage

2020 ◽  
Vol 100 (4) ◽  
pp. 703-715
Author(s):  
Shanwei Xu ◽  
Lysiane Dunière ◽  
Brenda Smiley ◽  
William Rutherford ◽  
Samuel Qi ◽  
...  
Keyword(s):  
Microbial Ecology ◽  
Lactobacillus Casei ◽  
Illumina Miseq ◽  
Miseq Sequencing ◽  
The Core ◽  
Aerobic Stability ◽  
Molecular Microbial Ecology ◽  
Differential Responses ◽  
Barley Silage ◽  
The Impact

Previously, we investigated the impact of a mixed Lactobacillus buchneri, Lactobacillus plantarum, and Lactobacillus casei inoculant on fermentation and aerobic stability of barley silage over two years in 2009 and 2010. In 2009, a classical response to inoculation was obtained with an increase in acetic acid concentration of silage ensiled in both mini- and bag silos. In 2010, this classical response was not observed in mini-silos but was observed in bag silos. The objective of this study was to determine if molecular microbial ecology could explain the differential responses to the inoculation of barley silage between the two years. The Illumina MiSeq sequencing results showed that inoculation increased Lactobacillus and lowered Pediococcus, Weissella, and Leuconostoc in both types of silos in 2009. However, a similar trend was not observed in mini-silos, but was instead observed in bag silos in 2010. Inoculation did not alter the core fungal community in either silo type in either year. Cladosporium, Leptosphaeria, and Cryptococcus were abundant in fresh forage, but were superseded by Pichia and Kazachstania after ensiling. Our results suggest that changes in silage chemistry corresponded to differences observed in microbial ecology. Inoculation may have less impact when using more mature crops with shorter ensiling times.

Effect of Drought and Recovery on Grazing Animal, Microbial, and Fungal Response in a Diverse Multi-Crop Rotation

2020 ◽  
Author(s):  
Douglas Landblom ◽  
Songul Senturklu
Keyword(s):  
Nutrient Cycling ◽  
Beef Cattle ◽  
Microbial Activity ◽  
Crop Rotation ◽  
Cover Crop ◽  
Crop Production ◽  
Microbial Respiration ◽  
Soil Nutrient ◽  
Soil Microbial ◽  
Animal Grazing

<p>Beef cattle grazing, soil microbial respiration, and Rhizobia spp. populations serve important roles in soil nutrient cycling and during periods of drought, when abnormal precipitation declines, forage production for animal grazing and performance are negatively impacted. Soil nutrient availability is essential for adequate crop production and extended drought reduces soil microbial activity and therefore nutrient cycling. During the 2017 growing season between April and October in the northern Great Plains region of the USA, effective precipitation for crop production and animal grazing was severely reduced due an exceptional drought as classified by the US Drought Monitor. At the NDSU – Dickinson Research Extension Center, Dickinson, North Dakota, USA, a long-term integrated system that includes yearling steer grazing within a diverse multi-crop rotation (spring wheat, cover crop, corn, pea-barley intercrop, and sunflower). Within the rotation of cash and forage crops, beef cattle graze the pea-barley, corn, and cover crop (13-specie) within the rotation and is being utilized to monitor the effects of animal, microbial and fungal activity over time and space in the crop and animal production system. Nitrogen fertilizer has been replaced in the system by soil microbial and fungal activity (Potential Mineralizable Nitrogen: 8.4 mg N/kg) such that for each 1% increase in SOM there is a corresponding increase of 18.8 kg of potential nitrogen mineralized per ha. Animal grazing days are severely reduced when precipitation is inadequate for soil microbial respiration to occur. What is even more concerning, when relying on microbial activity to supply plant nutrients, is recovery time for microbial activity to fully recover from exceptional drought as was the case in this research project. Compared to the 2016 crop production year that preceded the 2017 drought, cover crop (13-specie), pea-barley, and corn yields were reduced 86, 33, and 64% during the 2017 drought. This decline in crop production reduced the number of days of grazing by an average 50% and average daily gains were also reduced. Steer average daily gains were 1.05 0.95, and 0.83 kg/steer/day in 2017 when grazing pea-barley, corn, and cover crop, respectively. For this research that relies on soil derived plant nutrients soil analysis for microbial and Rhizobia spp. biomass began recovery in 2018 and continued into 2019 as evidenced by large percentage increases in organism biomass; however, complete production recovery did not occur by the end of the 2019 grazing season in which days of grazing were reduced compared to the 2016 grazing season. Biological animal, crop, microbial, fungal, and nutrient replacement recovery will be presented in the poster.</p>

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