Abundance and Diversity of CO2-Assimilating Bacteria and Algae Within Red Agricultural Soils Are Modulated by Changing Management Practice

The various fungal communities that adhere to apple fruit are influenced by agricultural practices. However, the effects of fruit bagging-based management practice on the fungal microbiota are still unknown, and little is known about the fungal communities of bagged apple fruit. We conducted a study using apple fruit grown in a conventionally managed orchard where pesticide use is an indispensable practice. Fungal communities were collected from the calyx-end and peel tissues of bagged and unbagged fruit and characterized using barcode-type next-generation sequencing. Fruit bagging had a stronger effect on fungal richness, abundance, and diversity of the fungal microbiota in comparison to non-bagging. In addition, bagging also impacted the compositional variation of the fungal communities inhabiting each fruit part. We observed that fruit bagging had a tendency to maintain ecological equilibrium since Ascomycota and Basidiomycota were more distributed in bagged fruit than in unbagged fruit. These fungal communities consist of beneficial fungi rather than potentially harmful fungi. Approximately 50 dominant taxa were detected in bagged fruit, for example, beneficial genera such as Articulospora, Bullera, Cryptococcus, Dioszegia, Erythrobasidium, and Sporobolomyces, as well as pathogenic genera such as Aureobasidium and Taphrina. These results suggested that fruit bagging could significantly increase fungal richness and promote healthy fungal communities, especially the harmless fungal communities, which might be helpful for protecting fruit from the effects of pathogens. This study provides a foundation for understanding the impacts of bagging-based practice on the associated fungal microbiota.

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Response of Soil Nematodes Under Different Pest Management Practices: A Field Experimental Approach in Tomato (Lycopersicon Esculentum L.) Growing Agro-Ecosystem

Journal of Institute of Science and Technology ◽

10.3126/jist.v22i2.19593 ◽

2018 ◽

Vol 22 (2) ◽

pp. 45-55

Author(s):

Dipak Gupta ◽

Daya Ram Bhusal

Keyword(s):

Lycopersicon Esculentum ◽

Pest Management ◽

Management Practices ◽

Community Dynamics ◽

Management Practice ◽

Winter Season ◽

Soil Nematodes ◽

Soil Biodiversity ◽

Abundance And Diversity ◽

And Control

The need of eco-friendly pest management practice is important to maintain soil biodiversity and sustainable agriculture. Therefore rigorous investigation is needed for the environmentally friendly pest management techniques worldwide including Nepalese Tomato growing farms. We conducted field experiment to monitor the diversity and community structure of soil nematodes under different pest management practices in Tomato (Lycopersicon esculentum) growing farm. The study was conducted during summer and winter season in 2015 in Tokha area of Northern part of Kathmandu valley. The field was designed as Urine mixture plot (MP), Pesticides plot (PP), Botanicals plots (BP) and Control plot (CP). Our result indicated the variation of abundance and diversity of nemato-fauna with treatment plots and seasons. The generic diversity and community composition of nematodes in Urine mixture treating plots (MP) was increased significantly whereas decreased in pesticide applying plot (PP). The F/B ratio was significantly affected with treatment system rather than seasonality and found to be increased in pesticides applying plots. The abundance samples of nematodes genera were well separated in our discriminate ordination. We highlight the need of further exploration on the diversity and community dynamics of soil nematodes under different pest management practices in Tomato growing Nepalese agro-farms for sustainable soil ecosystem service. Journal of Institute of Science and Technology Volume 22, Issue 2, January 2018, Page: 45-55

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Australian Soil Fertility Manual

10.1071/9780643100725 ◽

2006 ◽

Cited By ~ 4

Keyword(s):

Soil Fertility ◽

Environmental Fate ◽

Agricultural Soils ◽

Management Practice ◽

Management Strategies ◽

Biological Properties ◽

Plant Nutrients ◽

Nitrogen And Phosphorus ◽

Additional Information ◽

Australian Soil

The Australian Soil Fertility Manual is a trusted guide to the safe use and handling of fertilizers. It describes the types of agricultural soils, how they are classified and the interaction of soil, water and nutrients. It also provides an insight into how plants utilise nutrients and the role that individual nutrients play in the process of plant growth. This edition has been revised to reflect an increased emphasis on the environmental fate of nutrients and appropriate management strategies. It also has additional information on soil physical, chemical, and biological properties and discussions on the use of lime, dolomite and gypsum. New content covers liming effectiveness, nitrogen water use efficiency, regulations for handling and using fertilizers, storage and transport of security sensitive ammonium nitrate, budgeting for profitable nitrogen use and best management practice for nitrogen and phosphorus fertilizers. The chapters on potassium; calcium, magnesium and sulfur; plant nutrients and the environment; and heavy metal in fertilizers and agriculture have all been extensively revised and rewritten. This important work will be an essential text for fertilizer dealers, extension workers, consultants, teachers, farmers, horticulturists, graziers and others concerned with the profitable and environmentally safe use of plant nutrients.

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High arsenic levels increase activity rather than diversity or abundance of arsenic metabolism genes in paddy soils

10.21203/rs.3.rs-142737/v2 ◽

2021 ◽

Author(s):

Si-Yu Zhang ◽

Xiao Xiao ◽

Song-Can Chen ◽

Yong-Guan Zhu ◽

Konstantinos T. Konstantinidis

Keyword(s):

Transcriptional Activity ◽

Agricultural Soils ◽

Geographic Distance ◽

Environmental Pollutant ◽

Paddy Soils ◽

As Species ◽

Toxic Metalloid ◽

High Concentrations ◽

Abundance And Diversity ◽

Transcriptome Level

Abstract Arsenic (As) metabolism genes are generally present in soils but their diversity, relative abundance, and transcriptional activity in response to different As concentrations remain unclear, limiting our understanding of the microbial activities that control the fate of an important environmental pollutant. To address this issue, we applied metagenomics and metatranscriptomics to paddy soils showing a gradient of As concentrations to investigate As resistance genes (ars) including arsR, acr3, arsB, arsC, arsM, arsI, arsP, and arsH as well as energy-generating As respiratory oxidation (aioA) and reduction (arrA) genes. Somewhat unexpectedly, the relative DNA abundances and diversity of ars, aioA, and arrA genes were not significantly different between low and high (~10 vs ~100 mg kg-1) As soils. By comparison to available metagenomes from other soils, geographic distance rather than As levels drove the different compositions of microbial communities. Arsenic significantly increased ars genes abundance only when its concentration was higher than 410 mg kg-1. In contrast, between low and high As soils, metatranscriptomics revealed a significant increase in transcription of ars and aioA genes, which are induced by arsenite, the dominant As species in paddy soils, but not arrA genes, which are induced by arsenate. These patterns appeared to be community-wide as opposed to taxon-specific. Collectively, our findings advance understanding of how microbes respond to high As levels and the diversity of As metabolism genes in paddy soils and indicated that future studies of As metabolism in soil, or other environments, should include the function (transcriptome) level. IMPORTANCEArsenic (As) is a toxic metalloid pervasively present in the environment. Microorganisms have evolved the capacity to metabolize As, and As metabolism genes are ubiquitously present in the environment even in the absence of high concentrations of As. However, these previous studies were carried out at the DNA level and thus, the activity of the As metabolism genes detected remains essentially speculative. Here, we show that the high As levels in paddy soils increased the transcriptional activity rather than the relative DNA abundance and diversity of As metabolism genes. These findings advance our understanding of how microbes respond to and cope with high As levels and have implications for better monitoring and managing an important toxic metalloid in agricultural soils and possibly other ecosystems.

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Abundance and Diversity of Viruses in Six Delaware Soils

Applied and Environmental Microbiology ◽

10.1128/aem.71.6.3119-3125.2005 ◽

2005 ◽

Vol 71 (6) ◽

pp. 3119-3125 ◽

Cited By ~ 150

Author(s):

Kurt E. Williamson ◽

Mark Radosevich ◽

K. Eric Wommack

Keyword(s):

Land Use ◽

Forest Soils ◽

Agricultural Soils ◽

Dry Weight ◽

Morphological Data ◽

Epifluorescence Microscopy ◽

Viral Abundance ◽

Wide Range ◽

Virus Communities ◽

Abundance And Diversity

ABSTRACT The importance of viruses in marine microbial ecology has been established over the past decade. Specifically, viruses influence bacterial abundance and community composition through lysis and alter bacterial genetic diversity through transduction and lysogenic conversion. By contrast, the abundance and distribution of viruses in soils are almost completely unknown. This study describes the abundance and diversity of autochthonous viruses in six Delaware soils: two agricultural soils, two coastal plain forest soils, and two piedmont forest soils. Viral abundance was measured using epifluorescence microscopy, while viral diversity was assessed from morphological data obtained through transmission electron microscopy. Extracted soil virus communities were dominated by bacteriophages that demonstrated a wide range of capsid diameters (20 nm to 160 nm) and morphologies, including filamentous forms and phages with elongated capsids. The reciprocal Simpson's index suggests that forest soils harbor more diverse assemblages of viruses, particularly in terms of morphological distribution. Repeated extractions of virus-like particles (VLPs) from soils indicated that the initial round of extraction removes approximately 70% of extractable viruses. Higher VLP abundances were observed in forest soils (1.31 × 109 to 4.17 × 109 g−1 dry weight) than in agricultural soils (8.7 × 108 to 1.1 × 109 g−1 dry weight). Soil VLP abundance was significantly correlated to moisture content (r = 0.988) but not to soil texture. Land use (agricultural or forested) was significantly correlated to both bacterial (r = 0.885) and viral (r = 0.812) abundances, as were soil organic matter and water content. Thus, land use is a significant factor influencing viral abundance and diversity in soils.

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High arsenic levels increase activity rather than diversity or abundance of arsenic metabolism genes in paddy soils

Applied and Environmental Microbiology ◽

10.1128/aem.01383-21 ◽

2021 ◽

Author(s):

Si-Yu Zhang ◽

Xiao Xiao ◽

Song-Can Chen ◽

Yong-Guan Zhu ◽

Guo-Xin Sun ◽

...

Keyword(s):

Transcriptional Activity ◽

Agricultural Soils ◽

Geographic Distance ◽

Environmental Pollutant ◽

Paddy Soils ◽

As Species ◽

Toxic Metalloid ◽

High Concentrations ◽

Abundance And Diversity ◽

Transcriptome Level

Arsenic (As) metabolism genes are generally present in soils but their diversity, relative abundance, and transcriptional activity in response to different As concentrations remain unclear, limiting our understanding of the microbial activities that control the fate of an important environmental pollutant. To address this issue, we applied metagenomics and metatranscriptomics to paddy soils showing a gradient of As concentrations to investigate As resistance genes ( ars ) including arsR , acr3 , arsB , arsC , arsM , arsI , arsP , and arsH as well as energy-generating As respiratory oxidation ( aioA ) and reduction ( arrA ) genes. Somewhat unexpectedly, the relative DNA abundances and diversity of ars , aioA , and arrA genes were not significantly different between low and high (∼10 vs ∼100 mg kg −1 ) As soils. By comparison to available metagenomes from other soils, geographic distance rather than As levels drove the different compositions of microbial communities. Arsenic significantly increased ars genes abundance only when its concentration was higher than 410 mg kg −1 . In contrast, between low and high As soils, metatranscriptomics revealed a significant increase in transcription of ars and aioA genes, which are induced by arsenite, the dominant As species in paddy soils, but not arrA genes, which are induced by arsenate. These patterns appeared to be community-wide as opposed to taxon-specific. Collectively, our findings advance understanding of how microbes respond to high As levels and the diversity of As metabolism genes in paddy soils and indicated that future studies of As metabolism in soil, or other environments, should include the function (transcriptome) level. IMPORTANCE Arsenic (As) is a toxic metalloid pervasively present in the environment. Microorganisms have evolved the capacity to metabolize As, and As metabolism genes are ubiquitously present in the environment even in the absence of high concentrations of As. However, these previous studies were carried out at the DNA level and thus, the activity of the As metabolism genes detected remains essentially speculative. Here, we show that the high As levels in paddy soils increased the transcriptional activity rather than the relative DNA abundance and diversity of As metabolism genes. These findings advance our understanding of how microbes respond to and cope with high As levels and have implications for better monitoring and managing an important toxic metalloid in agricultural soils and possibly other ecosystems.

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Temporal shifts of nitrite reducing communities in a rice field soil in Ibague (Colombia)

Agronomía Colombiana ◽

10.15446/agron.colomb.v34n1.52993 ◽

2016 ◽

Vol 34 (1) ◽

pp. 82-91 ◽

Cited By ~ 2

Author(s):

Maribeb Castro-González ◽

Amanda Lima

Keyword(s):

Community Composition ◽

Rice Field ◽

Agricultural Soils ◽

Polymorphism Analysis ◽

Field Soil ◽

Operational Taxonomic Units ◽

Rice Field Soil ◽

Uncultivated Soil ◽

Abundance And Diversity ◽

Key Steps

Denitrification and nitrification are microbial processes that regulate the cycle of nitrogen and nitrous oxide, which is considered an important greenhouse gas. Rice field soils have been known to have strong denitrifying activities; however, the microorganism structure that is responsible for denitrification and the temporal variation of these communities in the agricultural soils of Ibague (Colombia) is not well known. In this study, the denitrifying community composition was compared between a rice field soil and an uncultivated soil at three different times during the year using a terminal restriction fragment length polymorphism analysis of the nirS functional gene, which codes the enzyme that reduces nitrite, one of the key steps in the denitrification process. The results showed changes in the richness, relative abundance and diversity of the operational taxonomic units between the soils and sampling times. The canonical correspondence analysis indicated that the moisture and the pH were the environmental factors that explained the observed changes in the nirS-type denitrifiers' community composition in the studied soils.

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Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set

10.1101/492488 ◽

2018 ◽

Cited By ~ 1

Author(s):

Zhirong Zhao ◽

Guohe Huang ◽

Mingyuan Wang ◽

Nan Zhou ◽

Shishi He ◽

...

Keyword(s):

Agricultural Soils ◽

River Sediments ◽

High Specificity ◽

Single Step ◽

Ammonia Oxidizing Bacteria ◽

Water And Wastewater Treatment ◽

Universal Primer ◽

Real Time Quantitative Pcr ◽

Clade B ◽

Abundance And Diversity

AbstractComplete ammonia oxidizing bacteria (CAOB) have been recognized as a new member of ammonia-oxidizing microorganisms (AOMs) due to its single-step nitrification capability. However, the abundance and diversity of CAOB in environmental ecosystems were still far from known owing to the lack of specific molecular marker. Herein, a universal primer set specifically targeting the both clades of CAOBamoAgene with high specificity and coverage was successfully designed. Intriguingly, real-time quantitative PCR tests revealed that CAOB were ubiquitous and unexpectedly abundant in agricultural soils, river sediments, intertidal zones, drinking water and wastewater treatment systems. Phylogenetic analysis indicated that clade A existed in all the five types of ecosystems, while clade B were only detected in soil and sediment samples. Four sub-clusters were further classified within clade A, in whichN. nitrosacluster dominated CAOBamoAin activated sludge samples while the new recognized soil cluster was the primary constitute in soils. Moreover, the niche specialization between different CAOB species and the environmental conditions were supposed to be the primary driven force to shape the diversity and community of CAOB. This study provided a strong evidence in support of the ubiquities and high abundances of CAOB in various environmental ecosystems and highlighted the significance of including CAOB as the new member of AOMs to re-evaluate the biogeochemical nitrogen cycle.

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