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Linking Soil Biology to Agro-Ecosystems Functional Sustainability

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A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: closed (1 May 2021) | Viewed by 34739

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Special Issue Editors

Dr. Nic Pacini

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Guest Editor

Department of Environmental Engineering, University of Calabria, 87036 Arcavacata di Rende, Italy
Interests: tropical ecology; soil ecology; biogeochemistry; community ecology
Special Issues, Collections and Topics in MDPI journals

Dr. Edoardo Puglisi

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Guest Editor

Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, 20123 Milan, Italy
Interests: microbial ecotoxicology of microplastics in soils and gut; biodegradation; anaerobic digestion and composting of bioplastics; terrestrial plastisphere; culturomics of plastic degrading bacteria and fungi

Special Issue Information

Dear Colleagues,

Soil bacteria and fungi provide essential soil ecosystem services supporting agricultural production. The collation of case studies presented in this issue will illustrate how the structure, composition, and activity of soil bacteria and fungi is related to farming practices, including crop rotation, tillage, fertilization, irrigation, application of plant protection products, etc., to the choice of crops and the ecosystem services delivered in agricultural landscapes. Studies applying metagenomic techniques to provide details of soil communities, including bacteria, fungi, and also mesofauna and pollinator insects, are welcome, as well as enzymatic analyses highlighting microbial function. We seek articles providing evidence of interactions between activities of soil microbes and mesofauna and soil biogeochemistry, including nutrient cycling and the formation and release of greenhouse gases, and recommendation proposals that may lead to optimized soil management practices. Particular attention will be dedicated to contributions highlighting the adaptation of the soil community to stress caused by pollution, drought, pesticide residues, excessive compaction, acidification, and other human impacts that typically affect the sustainability of farming operations under the impact of global changes. The issue is open to case studies from any part of the world.

Dr. Nic Pacini
Prof. Edoardo Puglisi
Guest Editors

Manuscript Submission Information

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Keywords

soil microbiological processes
microbial activity indices
diversity of soil bacteria and fungi
impact of farming on soil biology
crop-microbe interactions
climate change impact on soils
effects on ecosystem services

Published Papers (5 papers)

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Research

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14 pages, 1952 KiB

Open AccessArticle

Combined Effect of Laboratory-Simulated Fire and Chromium Pollution on Microbial Communities in an Agricultural Soil

by Ida Rascio, Maddalena Curci, Concetta Eliana Gattullo, Anna Lavecchia, Mohammad Yaghoubi Khanghahi, Roberto Terzano and Carmine Crecchio

Biology 2021, 10(7), 587; https://0-doi-org.brum.beds.ac.uk/10.3390/biology10070587 - 26 Jun 2021

Cited by 7 | Viewed by 1964

Abstract

Fire events in agricultural soils can modify not only soil properties but also the structure of soil microbial communities, especially in soils containing high concentrations of potentially toxic elements (PTEs). The recolonization of burned soils can in fact favor the proliferation of certain microorganisms, more adaptable to post-fire soil conditions and higher PTE availability, over others. In this study, we simulated with laboratory experiments the microbial recolonization of an agricultural soil containing high Cr concentrations after heating at 500 °C for 30 min, to mimic the burning of crop residues. Changes in soil properties and Cr speciation were assessed, as well as soil microbial structure by means of 16S rRNA gene sequencing. Both altered soil conditions and increased Cr availability, especially Cr(VI), appeared to be responsible for the reduction in species diversity in heated soils and the proliferation of Firmicutes. Indeed, already after 3 days from the heat treatment, Firmicutes increased from 14% to 60% relative abundance. In particular, Paenibacillus was the most abundant genus identified after the simulation, with an average relative abundance of 40%. These bacteria are known to be good fire-responders and Cr-tolerant. These results could be useful to identify bacterial strains to be used as bioindicators of altered environments and for the recovery of fire-impacted polluted sites. Full article

(This article belongs to the Special Issue Linking Soil Biology to Agro-Ecosystems Functional Sustainability)

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12 pages, 1018 KiB

Open AccessArticle

Evaluation of Sown Cover Crops and Spontaneous Weed Flora as a Potential Reservoir of Black-Foot Pathogens in Organic Viticulture

by Maela León, Mónica Berbegal, Paloma Abad-Campos, Antonio Ramón-Albalat, Tito Caffi, Vittorio Rossi, Gultakin Hasanaliyeva, Pierre Antoine Noceto, Daniel Wipf, Saša Širca, Jaka Razinger, Anne-Laure Fragnière, Patrik Kehrli, Aurora Ranca, Anamaria Petrescu and Josep Armengol

Biology 2021, 10(6), 498; https://0-doi-org.brum.beds.ac.uk/10.3390/biology10060498 - 03 Jun 2021

Cited by 3 | Viewed by 2228

Abstract

(1) Background. An extensive survey of grapevine-sown cover crops and spontaneous weed flora was conducted from 2019 to 2020 in organic vineyards in six European countries (France, Italy, Romania, Slovenia, Spain, Switzerland). Our main objective was to detect and identify the presence of Cylindrocarpon-like asexual morphs species associated with black-foot disease on their roots. (2) Methods. Fungal isolations from root fragments were performed on culture media. Cylindrocarpon-like asexual morph species were identified by analyzing the DNA sequence data of the histone H3 (his3) gene region. In all, 685 plants belonging to different botanical families and genera were analyzed. Cylindrocarpon-like asexual morphs were recovered from 68 plants (9.9% of the total) and approximately 0.97% of the plated root fragments. (3) Results. Three fungal species (Dactylonectria alcacerensis, Dactylonectria torresensis, Ilyonectria robusta) were identified. Dactylonectria torresensis was the most frequent, and was isolated from many cover crop species in all six countries. A principal component analysis with the vineyard variables showed that seasonal temperatures and organic matter soil content correlated positively with Cylindrocarpon-like asexual morphs incidence. (4) Conclusions. The presence of Cylindrocarpon-like asexual morphs on roots of cover crops suggests that they can potentially act as alternative hosts for long-term survival or to increase inoculum levels in vineyard soils. Full article

(This article belongs to the Special Issue Linking Soil Biology to Agro-Ecosystems Functional Sustainability)

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Graphical abstract

18 pages, 2737 KiB

Open AccessArticle

Smallholder Farmers’ Practices and African Indigenous Vegetables Affect Soil Microbial Biodiversity and Enzyme Activities in Lake Naivasha Basin, Kenya

by Eren Taskin, Chiara Misci, Francesca Bandini, Andrea Fiorini, Nic Pacini, Clifford Obiero, Daniel Ndaka Sila, Vincenzo Tabaglio and Edoardo Puglisi

Biology 2021, 10(1), 44; https://0-doi-org.brum.beds.ac.uk/10.3390/biology10010044 - 11 Jan 2021

Cited by 5 | Viewed by 3025

Abstract

Loss of soil biodiversity and fertility in Sub-Saharan Africa (SSA) may put the food security of smallholder farmers in peril. Food systems in SSA are seeing the rise of African indigenous vegetables (AIVs) that are underexploited but locally consumed without being considered a primary source of food and income. Here we present a field study, a first of its kind, in which we investigated the effects of different cropping systems and inclusion of AIVs in the farming approach on bacterial and fungal biodiversity and community structures, enzymatic activity, and the alteration status of soils of the smallholder farmers in Kenya. When compared to mainstream farming approaches, the composition and biodiversity of bacteria and fungi under AIV cultivations was significantly different. Tillage had a significant impact only on the fungal communities. Fertilization and soil amendments caused shifts in microbial communities towards specialized degraders and revealed the introduction of specific microorganisms from amendments. Traditional homemade plant protection products did not cause any disturbance to either of soil bacteria or fungi. The soil alteration index based on enzyme activity successfully differentiated the alteration status for the first time in SSA. These findings could be useful for farmers to integrate AIVs with correct sustainable practices for a sustainable future. Full article

(This article belongs to the Special Issue Linking Soil Biology to Agro-Ecosystems Functional Sustainability)

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19 pages, 2130 KiB

Open AccessEditor’s ChoiceArticle

Combined Impact of No-Till and Cover Crops with or without Short-Term Water Stress as Revealed by Physicochemical and Microbiological Indicators

by Eren Taskin, Roberta Boselli, Andrea Fiorini, Chiara Misci, Federico Ardenti, Francesca Bandini, Lorenzo Guzzetti, Davide Panzeri, Nicola Tommasi, Andrea Galimberti, Massimo Labra, Vincenzo Tabaglio and Edoardo Puglisi

Biology 2021, 10(1), 23; https://0-doi-org.brum.beds.ac.uk/10.3390/biology10010023 - 01 Jan 2021

Cited by 5 | Viewed by 2565

Abstract

Combining no-till and cover crops (NT + CC) as an alternative to conventional tillage (CT) is generating interest to build-up farming systems’ resilience while promoting climate change adaptation in agriculture. Our field study aimed to assess the impact of long-term NT + CC management and short-term water stress on soil microbial communities, enzymatic activities, and the distribution of C and N within soil aggregates. High-throughput sequencing (HTS) revealed the positive impact of NT + CC on microbial biodiversity, especially under water stress conditions, with the presence of important rhizobacteria (e.g., Bradyrhizobium spp.). An alteration index based on soil enzymes confirmed soil depletion under CT. C and N pools within aggregates showed an enrichment under NT + CC mostly due to C and N-rich large macroaggregates (LM), accounting for 44% and 33% of the total soil C and N. Within LM, C and N pools were associated to microaggregates within macroaggregates (mM), which are beneficial for long-term C and N stabilization in soils. Water stress had detrimental effects on aggregate formation and limited C and N inclusion within aggregates. The microbiological and physicochemical parameters correlation supported the hypothesis that long-term NT + CC is a promising alternative to CT, due to the contribution to soil C and N stabilization while enhancing the biodiversity and enzymes. Full article

(This article belongs to the Special Issue Linking Soil Biology to Agro-Ecosystems Functional Sustainability)

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Review

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19 pages, 2383 KiB

Open AccessReview

Roles of Phosphate Solubilizing Microorganisms from Managing Soil Phosphorus Deficiency to Mediating Biogeochemical P Cycle

by Jiang Tian, Fei Ge, Dayi Zhang, Songqiang Deng and Xingwang Liu

Biology 2021, 10(2), 158; https://0-doi-org.brum.beds.ac.uk/10.3390/biology10020158 - 17 Feb 2021

Cited by 143 | Viewed by 23894

Abstract

Phosphorus (P) is a vital element in biological molecules, and one of the main limiting elements for biomass production as plant-available P represents only a small fraction of total soil P. Increasing global food demand and modern agricultural consumption of P fertilizers could lead to excessive inputs of inorganic P in intensively managed croplands, consequently rising P losses and ongoing eutrophication of surface waters. Despite phosphate solubilizing microorganisms (PSMs) are widely accepted as eco-friendly P fertilizers for increasing agricultural productivity, a comprehensive and deeper understanding of the role of PSMs in P geochemical processes for managing P deficiency has received inadequate attention. In this review, we summarize the basic P forms and their geochemical and biological cycles in soil systems, how PSMs mediate soil P biogeochemical cycles, and the metabolic and enzymatic mechanisms behind these processes. We also highlight the important roles of PSMs in the biogeochemical P cycle and provide perspectives on several environmental issues to prioritize in future PSM applications. Full article

(This article belongs to the Special Issue Linking Soil Biology to Agro-Ecosystems Functional Sustainability)

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