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Microorganisms in Recycling and Valorization of Organic Waste for Sustainable Soil Health and Management

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (31 January 2021) | Viewed by 44649

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Dr. María Gómez-Brandón

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Guest Editor

Grupo de Ecoloxía Animal (GEA), Universidad de Vigo, E-36310 Vigo, Spain
Interests: microbial ecology; ecosystem functioning; soil biodiversity; soil microbiology; organic waste treatment; vermicomposting; anaerobic digestion; sustainable agriculture

Dr. José A. Siles

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Guest Editor

Department of Plant & Microbial Biology, University of California at Berkeley, Berkeley, CA, USA
Interests: soil biodiversity; soil microbial ecology; bioremediation; organic waste treatment; organic amendments; soil organic matter dynamics; carbon cycling

Dr. Mercedes Garcıá-Sánchez

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Guest Editor

INRA, UMR Eco&Sols, 2 Place Pierre Viala, 34060 Montpellier, France
Interests: soil functional ecology; microbial loop; organic amendments; phosphorus cycling; plant nutrition; degraded-soils; sustainable agriculture; ecosystems functioning

Special Issue Information

Dear Colleagues,

Agricultural intensification constitutes one of the most prevalent challenges of the twenty-first century because of continuous global population growth. This has given rise to several critical environmental concerns, such as enhanced greenhouse gas emissions and pesticide use, groundwater eutrophication, reduced aboveground biodiversity, degradation of soil quality, and soil erosion. The application of organic wastes as soil amendments has been proposed as an effective way of restoring soil fertility while at the same time protecting the environment. However, if not properly disposed of and treated, the use of raw wastes as soil inputs can be a serious threat to the environment. The adoption of biological approaches including composting, vermicomposting, or methanogenic processes may offer the possibility of stabilizing them before their use or disposal achieving a dual purpose, i.e., environmental protection and fertilizer production. Considering that the involvement of microorganisms in these processes is fundamental, we invite you to send contributions focusing on the characterization of microbial communities, from a taxonomic and functional perspective, involved in the dynamics of the abovementioned processes. Another crucial aspect to be considered within this Special Issue will be to evaluate the usefulness of raw and treated organic wastes (composts, vermicomposts, and digestates) as soil organic amendments. Special attention will be given to their impact on soil microbial communities (in terms of abundance, taxonomy, and functionality), nutrient cycling, and plant yields under field and greenhouse conditions so as to evaluate their role as bio-indicators of soil quality.

Dr. María Gómez-Brandón
Dr. José A. Siles
Dr. Mercedes Garcıá-Sánchez
Guest Editors

Manuscript Submission Information

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Keywords

sustainable agriculture
microbial communities
vermicomposting
composting
digestate
ecosystem functioning
sustainable waste management
soil nutrient cycling
organic amendments
soil health
bio-indicators

Published Papers (10 papers)

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Editorial

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3 pages, 197 KiB

Open AccessEditorial

Special Issue “Microorganisms in Recycling and Valorization of Organic Waste for Sustainable Soil Health and Management”

by José A. Siles, Mercedes García-Sánchez and María Gómez-Brandón

Microorganisms 2021, 9(8), 1682; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081682 - 08 Aug 2021

Cited by 1 | Viewed by 1692

Abstract

Anthropogenic activity generates huge amounts of solid organic wastes [...] Full article

(This article belongs to the Special Issue Microorganisms in Recycling and Valorization of Organic Waste for Sustainable Soil Health and Management)

Research

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21 pages, 1426 KiB

Open AccessArticle

Microbial Shifts Following Five Years of Cover Cropping and Tillage Practices in Fertile Agroecosystems

by Nakian Kim, María C. Zabaloy, Chance W. Riggins, Sandra Rodríguez-Zas and María B. Villamil

Microorganisms 2020, 8(11), 1773; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8111773 - 11 Nov 2020

Cited by 10 | Viewed by 2536

Abstract

Metagenomics in agricultural research allows for searching for bioindicators of soil health to characterize changes caused by management practices. Cover cropping (CC) improves soil health by mitigating nutrient losses, yet the benefits depend on the tillage system used. Field studies searching for indicator taxa within these systems are scarce and narrow in their scope. Our goal was to identify bioindicators of soil health from microbes that were responsive to CC (three levels) and tillage (chisel tillage, no-till) treatments after five years under field conditions. We used rRNA gene-based analysis via Illumina HiSeq2500 technology with QIIME 2.0 processing to characterize the microbial communities. Our results indicated that CC and tillage differentially changed the relative abundances (RAs) of the copiotrophic and oligotrophic guilds. Corn–soybean rotations with legume–grass CC increased the RA of copiotrophic decomposers more than rotations with grass CC, whereas rotations with only bare fallows favored stress-tolerant oligotrophs, including nitrifiers and denitrifiers. Unlike bacteria, fewer indicator fungi and archaea were detected; fungi were poorly identified, and their responses were inconsistent, while the archaea RA increased under bare fallow treatments. This is primary information that allows for understanding the potential for managing the soil community compositions using cover crops to reduce nutrient losses to the environment. Full article

(This article belongs to the Special Issue Microorganisms in Recycling and Valorization of Organic Waste for Sustainable Soil Health and Management)

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12 pages, 1766 KiB

Open AccessArticle

Bacterial Community Dynamics Distinguish Poultry Compost from Dairy Compost and Non-Amended Soils Planted with Spinach

by Deborah A. Neher, Marie A. Limoges, Thomas R. Weicht, Manan Sharma, Patricia D. Millner and Catherine Donnelly

Microorganisms 2020, 8(10), 1601; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8101601 - 18 Oct 2020

Cited by 11 | Viewed by 2556

Abstract

The aim of this study was to determine whether and how poultry litter compost and dairy manure compost alter the microbial communities within field soils planted with spinach. In three successive years, separate experimental plots on two fields received randomly assigned compost treatments varying in animal origin: dairy manure (DMC), poultry litter (PLC), or neither (NoC). The composition and function of bacterial and fungal communities were characterized by the amplicon sequencing of marker genes and by the ecoenzyme activity, respectively. The temporal autocorrelation within and among years was adjusted by principal response curves (PRC) to analyze the effect of compost on community composition among treatments. Bacteria in the phylum Bacteriodetes, classes Flavobacteriia and Spingobacteriales (Fluviicola, Flavobacteriia, and Pedobacter), were two to four times more abundant in soils amended with PLC than DMC or NoC consistently among fields and years. Fungi in the phylum Ascomycota were relatively abundant, but their composition was field-specific and without treatment differences. The ecoenzyme data verify that the effects of PLC and DMC on soil communities are based on their microbial composition and not a response to the C source or nutrient content of the compost. Full article

(This article belongs to the Special Issue Microorganisms in Recycling and Valorization of Organic Waste for Sustainable Soil Health and Management)

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25 pages, 1565 KiB

Open AccessArticle

Effects of Selected Functional Bacteria on Maize Growth and Nutrient Use Efficiency

by Amelia Tang, Ahmed Osumanu Haruna, Nik Muhamad Ab. Majid and Mohamadu Boyie Jalloh

Microorganisms 2020, 8(6), 854; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8060854 - 05 Jun 2020

Cited by 24 | Viewed by 4571

Abstract

Plant growth-promoting rhizobacteria (PGPR), which include isolates from genera Paraburkholderia, Burkholderia and Serratia, have received attention due to their numerous plant growth-promoting mechanisms such as their ability to solubilize insoluble phosphates and nitrogen-fixation. However, there is a dearth of information on the potential plant growth-promoting effects of these three groups of bacteria on non-legumes such as maize. This study determined the influences of the aforementioned strains on soil properties, maize growth, nutrient uptake and nutrient use efficiency. A pot trial using maize as a test crop was done using a randomized complete block design with 7 treatments each replicated 7 times. The treatments used in this study were: Control (no fertilizer), chemical fertilizer (CF), organic-chemical fertilizers combination without inoculum (OCF) and with inocula consisting of single strains [cellulolytic bacteria (TC), organic fertilizer and chemical fertilizer with N-fixing bacteria (TN), organic fertilizer and chemical fertilizer with P-solubilizing bacteria (TP)) and three-strain inocula (TCNP), respectively. The variables measured included plant growth and nutrient content, soil nutrient content and functional rhizospheric bacterial populations. Paraburkholderia nodosa NB1 and Burkholderia cepacia PB3 showed comparable effects on maize biomass and also improved N and P use efficiencies when compared to full chemical fertilization. Nitrogen-fixing rhizobacteria had a positive effect on above-ground biomass of maize. Paraburkholderia nodosa NB1 improved soil total C and organic matter contents, besides being the only bacterial treatment that improved K use efficiency compared to OCF. The results suggest that P. nodosa NB1 and B. cepacia PB3 have potential usage in bio-fertilizers. In contrast, treatments with Serratia nematodiphila C46d and consortium strains showed poorer maize nutrient uptake and use efficiency than the other single strain treatments. Bacterial treatments generally showed comparable or higher overall N and P use efficiencies than full chemical fertilization. These findings suggest that at least half the amounts of N and P fertilizers could be reduced through the use of combined fertilization together with beneficial bacteria. Full article

(This article belongs to the Special Issue Microorganisms in Recycling and Valorization of Organic Waste for Sustainable Soil Health and Management)

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8 pages, 842 KiB

Open AccessCommunication

Composting Reduces the Vitality of H9N2 in Poultry Manure and EMCV in Pig Manure Allowing for an Environmentally Friendly Use of These Animal Wastes: A Preliminary Study

by Kwang-Hwa Jeong, Dong-Jun Lee, Dong-Hyun Lee, Balasubramani Ravindran, Soon Woong Chang, Hupenyu Allan Mupambwa, Myung-Gyu Lee and Hee-Kwon Ahn

Microorganisms 2020, 8(6), 829; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8060829 - 31 May 2020

Cited by 7 | Viewed by 2672

Abstract

In our study, we monitored the inactivation of two important viruses that are critical in animal husbandry throughout the world. To evaluate the influence of the composting process on inactivation of avian influenza virus (H9N2) in poultry manure compost (PMC) and Encephalomyocarditis virus (EMCV) in pig (swine) manure compost (SMC), the H9N2 and EMCV were injected in dialysis cassettes and buried in two different manure compost piles of poultry and pig manure, respectively. The highest temperature achieved in the PMC and SMC piles during the test period were 75 °C and 73.5 °C, respectively. At the completion of the composting for 168 h, inactivation effect appeared to be more sensitive in H9N2 than EMCV. The vitality of H9N2 decreased by 6.25 ± 0.35 log₁₀TCID50/mL to 0.0 log₁₀TCID50/mL within 1 h of the composting. The vitality of EMCV decreased from 7.75 ± 0.35 log₁₀TCID50/mL to 1.50 log₁₀TCID50/mL within 24 h of starting the composting process. However, the activation of EMCV was not decreased (from 7.75 ± 0.35 to 7.50 ± 0.71 log10TCID50/mL) in the control treatment (not inserted in composts) after 168h, while the activation of H9N2 in dialysis cassettes was significantly decreased (from 6.25 ± 0.35 log₁₀TCID50/mL to 2.00 ± 0.6 log₁₀TCID50/mL). Our study demonstrated the effectiveness of the composting treatment in inactivating the viruses studied, which was not the case with air treatment. Full article

(This article belongs to the Special Issue Microorganisms in Recycling and Valorization of Organic Waste for Sustainable Soil Health and Management)

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22 pages, 5864 KiB

Open AccessArticle

Soil Chemical and Microbiological Properties Are Changed by Long-Term Chemical Fertilizers That Limit Ecosystem Functioning

by Yong-Chao Bai, Ying-Ying Chang, Muzammil Hussain, Bin Lu, Jun-Pei Zhang, Xiao-Bo Song, Xia-Shuo Lei and Dong Pei

Microorganisms 2020, 8(5), 694; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8050694 - 08 May 2020

Cited by 82 | Viewed by 6715

Abstract

Although the effects of fertilization and microbiota on plant growth have been widely studied, our understanding of the chemical fertilizers to alter soil chemical and microbiological properties in woody plants is still limited. The aim of the present study is to investigate the impact of long-term application of chemical fertilizers on chemical and microbiological properties of root-associated soils of walnut trees. The results show that soil organic matter (OM), pH_kcl, total nitrogen (TN), nitrate-nitrogen (NO₃⁻), and total phosphorus (TP) contents were significantly higher in non-fertilized soil than after chemical fertilization. The long-term fertilization led to excessive ammonium-nitrogen (NH₄⁺) and available phosphorus (AP) residues in the cultivated soil, among which NH₄⁺ resulted in soil acidification and changes in bacterial community structure, while AP reduced fungal diversity. The naturally grown walnut trees led to an enrichment in beneficial bacteria such as Burkholderia, Nitrospira, Pseudomonas, and Candidatus_Solibacter, as well as fungi, including Trichoderma, Lophiostoma, Phomopsis, Ilyonectria, Purpureocillium, Cylindrocladiella, Hyalorbilia, Chaetomium, and Trichoglossum. The presence of these bacterial and fungal genera that have been associated with nutrient mobilization and plant growth was likely related to the higher soil OM, TN, NO₃⁻, and TP contents in the non-fertilized plots. These findings highlight that reduced chemical fertilizers and organic cultivation with beneficial microbiota could be used to improve economic efficiency and benefit the environment in sustainable agriculture. Full article

(This article belongs to the Special Issue Microorganisms in Recycling and Valorization of Organic Waste for Sustainable Soil Health and Management)

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19 pages, 3797 KiB

Open AccessArticle

Temporal Dynamics of Bacterial Communities in a Pilot-Scale Vermireactor Fed with Distilled Grape Marc

by María Gómez-Brandón, Manuel Aira, Natielo Santana, Marcos Pérez-Losada and Jorge Domínguez

Microorganisms 2020, 8(5), 642; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8050642 - 28 Apr 2020

Cited by 14 | Viewed by 2722

Abstract

Vermicomposting has been found as a profitable approach to dispose of and treat large quantities of raw grape marc. However, less information is available with regard to its efficiency for treating distillery winery byproducts, even though distillation has been widely used as a way to economically valorize grape marc. As such, we sought to characterize the compositional and functional changes in bacterial communities during vermicomposting of distilled grape marc by using 16S rRNA high-throughput sequencing. Samples were collected at the initiation of vermicomposting and at days 14, 21, 28, 35 and 42. There were significant changes (p < 0.0001) in the bacterial community composition of distilled grape marc after 14 days of vermicomposting that were accompanied by twofold increases in bacterial richness and diversity from a taxonomic and phylogenetic perspective. This was followed by significant increases in functional diversity of the bacterial community, including metabolic capacity, lignin and cellulose metabolism, and salicylic acid synthesis. These findings indicate that the most striking compositional and functional bacterial community changes took place during the active phase of the process. They also pinpoint functional attributes that may be related to the potential beneficial effects of distilled grape marc vermicompost when applied on soil and plants. Full article

(This article belongs to the Special Issue Microorganisms in Recycling and Valorization of Organic Waste for Sustainable Soil Health and Management)

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12 pages, 1743 KiB

Open AccessArticle

Effect of Thermal Drying and Chemical Treatments with Wastes on Microbiological Contamination Indicators in Sewage Sludge

by Andreia F. Santos, Cátia P. Santos, Ana M. Matos, Olga Cardoso and Margarida J. Quina

Microorganisms 2020, 8(3), 376; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8030376 - 07 Mar 2020

Cited by 16 | Viewed by 2992

Abstract

This work aims to evaluate the microbiological contamination of sewage sludge (SS) collected in urban wastewater treatment plants (WWTP) from Portugal. Two types of SS were considered: urban mixed (UM) and from anaerobic digestion (AD). The two types of samples were characterized in relation to the main physical and chemical parameters, as well as the microbiological contamination (Escherichia coli and Salmonella spp). Then, sanitation tests were conducted through thermal drying and chemical treatments. Towards a circular economy, industrial alkaline wastes (green liquor dregs - GLD, lime mud, coal fly ash, eggshell) were tested as alternatives to lime. Only six out of nineteen samples complied with the legal limits for both microorganisms. However, drying at 130 °C sanitized selected samples below the E. coli limit, regardless of the initial moisture or contamination. Additionally, CaO (obtained from eggshell) led to the complete elimination of E. coli at any dosage studied (0.05–0.15 g/g SS_{wet basis}). GLD evidenced the ability to reduce E. coli contamination at room temperature, but not enough to comply with the legal limit. In general, this work highlights the need to sanitize the SS before its application to the soil, and the positive role of some wastes on this goal. Full article

(This article belongs to the Special Issue Microorganisms in Recycling and Valorization of Organic Waste for Sustainable Soil Health and Management)

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Review

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15 pages, 634 KiB

Open AccessReview

Studying Microbial Communities through Co-Occurrence Network Analyses during Processes of Waste Treatment and in Organically Amended Soils: A Review

by José A. Siles, Mercedes García-Sánchez and María Gómez-Brandón

Microorganisms 2021, 9(6), 1165; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9061165 - 28 May 2021

Cited by 19 | Viewed by 4638

Abstract

Organic wastes have the potential to be used as soil organic amendments after undergoing a process of stabilization such as composting or as a resource of renewable energy by anaerobic digestion (AD). Both composting and AD are well-known, eco-friendly approaches to eliminate and recycle massive amounts of wastes. Likewise, the application of compost amendments and digestate (the by-product resulting from AD) has been proposed as an effective way of improving soil fertility. The study of microbial communities involved in these waste treatment processes, as well as in organically amended soils, is key in promoting waste resource efficiency and deciphering the features that characterize microbial communities under improved soil fertility conditions. To move beyond the classical analyses of metataxonomic data, the application of co-occurrence network approaches has shown to be useful to gain insights into the interactions among the members of a microbial community, to identify its keystone members and modelling the environmental factors that drive microbial network patterns. Here, we provide an overview of essential concepts for the interpretation and construction of co-occurrence networks and review the features of microbial co-occurrence networks during the processes of composting and AD and following the application of the respective end products (compost and digestate) into soil. Full article

(This article belongs to the Special Issue Microorganisms in Recycling and Valorization of Organic Waste for Sustainable Soil Health and Management)

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18 pages, 8857 KiB

Open AccessReview

Effects of Organic Fertilizers on the Soil Microorganisms Responsible for N₂O Emissions: A Review

by Cristina Lazcano, Xia Zhu-Barker and Charlotte Decock

Microorganisms 2021, 9(5), 983; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9050983 - 01 May 2021

Cited by 64 | Viewed by 11322

Abstract

The use of organic fertilizers constitutes a sustainable strategy to recycle nutrients, increase soil carbon (C) stocks and mitigate climate change. Yet, this depends largely on balance between soil C sequestration and the emissions of the potent greenhouse gas nitrous oxide (N₂O). Organic fertilizers strongly influence the microbial processes leading to the release of N₂O. The magnitude and pattern of N₂O emissions are different from the emissions observed from inorganic fertilizers and difficult to predict, which hinders developing best management practices specific to organic fertilizers. Currently, we lack a comprehensive evaluation of the effects of OFs on the function and structure of the N cycling microbial communities. Focusing on animal manures, here we provide an overview of the effects of these organic fertilizers on the community structure and function of nitrifying and denitrifying microorganisms in upland soils. Unprocessed manure with high moisture, high available nitrogen (N) and C content can shift the structure of the microbial community, increasing the abundance and activity of nitrifying and denitrifying microorganisms. Processed manure, such as digestate, compost, vermicompost and biochar, can also stimulate nitrifying and denitrifying microorganisms, although the effects on the soil microbial community structure are different, and N₂O emissions are comparatively lower than raw manure. We propose a framework of best management practices to minimize the negative environmental impacts of organic fertilizers and maximize their benefits in improving soil health and sustaining food production systems. Long-term application of composted manure and the buildup of soil C stocks may contribute to N retention as microbial or stabilized organic N in the soil while increasing the abundance of denitrifying microorganisms and thus reduce the emissions of N₂O by favoring the completion of denitrification to produce dinitrogen gas. Future research using multi-omics approaches can be used to establish key biochemical pathways and microbial taxa responsible for N₂O production under organic fertilization. Full article

(This article belongs to the Special Issue Microorganisms in Recycling and Valorization of Organic Waste for Sustainable Soil Health and Management)

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