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14 pages, 3320 KiB

Open AccessArticle

Changes in the Bacterial Community Composition of Cultivated Soil after Digging up Operations for Laying a Pipeline

by Maria Grazia Bonomo, Laura Scrano, Stefania Mirela Mang, Barbara Emanuela Scalese, Sabino Aurelio Bufo, Lee-Ann Modley, Euro Buongarzone and Giovanni Salzano

Agriculture 2023, 13(6), 1189; https://doi.org/10.3390/agriculture13061189 - 02 Jun 2023

Viewed by 1097

Abstract

Our study aimed to evaluate the impact of the pipeline installation on the bacterial composition in cultivated soil by metagenomic analyses performed before the excavation and in the following three years. Differential abundance analysis was obtained using DESeq2 from the GAIA pipeline to [...] Read more.

Our study aimed to evaluate the impact of the pipeline installation on the bacterial composition in cultivated soil by metagenomic analyses performed before the excavation and in the following three years. Differential abundance analysis was obtained using DESeq2 from the GAIA pipeline to verify the bacteriological diversity in soils collected after the reference year (2013). Soil samples presented a different distribution of taxa, especially in 2014, in which a further allocation at the phylum and family levels was observed compared to the previous year (2013). The phyla Bacteroidetes and Firmicutes increased significantly, while the phylum Actinobacteria, most abundant in 2013, showed reduced abundance; moreover, Chloroflexi and Planctomycetes decreased considerably, and Verrucomicrobia was absent. The significant differences in the taxonomic composition and structure of the soil microbial community were due to critical stress conditions following the soil excavations. The bacterial communities were capable of profound physiological and genetic changes, implementing different mechanisms for survival and adaptation to an environment with changed conditions. The implication of changes in microbial diversity before and after the mechanical insult of soil has been determined. Full article

(This article belongs to the Special Issue Advanced Research of Soil Microbial Functional Diversity)

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18 pages, 2625 KiB

Open AccessArticle

Sorption–Desorption of Imazamox and 2,4-DB in Acidic Mediterranean Agricultural Soils and Herbicide Impact on Culturable Bacterial Populations and Functional Diversity

by Maria V. Pinna, Paola Castaldi, Matteo Garau, Angela Bianco, Chiara Multineddu, Alberto Cesarani, Maria Sitzia, Stefania Diquattro, Nicoletta P. Mangia and Giovanni Garau

Agriculture 2022, 12(11), 1862; https://doi.org/10.3390/agriculture12111862 - 05 Nov 2022

Cited by 1 | Viewed by 1619

Abstract

In this study, we investigated the sorption–desorption behavior of imazamox (IMZ) and 2,4-DB (DB) in two typical acidic Mediterranean agricultural soils and the impact of these herbicides on culturable soil bacterial populations, enzyme activities and functional diversity when applied at concentrations higher than [...] Read more.

In this study, we investigated the sorption–desorption behavior of imazamox (IMZ) and 2,4-DB (DB) in two typical acidic Mediterranean agricultural soils and the impact of these herbicides on culturable soil bacterial populations, enzyme activities and functional diversity when applied at concentrations higher than recommended doses (10×, 50×, 500×). Herbicide sorption was similar in both soils and IMZ was less retained compared to DB (~0.5 vs. 40 µg g⁻¹ soil, respectively). IMZ desorption was remarkable (70–100%) while that of DB was more limited, i.e., ~40%. Three days after spiking (DAS), IMZ and DB significantly increased the number of soil-culturable heterotrophic bacteria, actinomycetes and Pseudomonas spp., soil respiration and the potential catabolic capacity of soil microbial communities. Soil dehydrogenase activity increased by ~56–70% in IMZ-treated soils while being reduced by ~33–41% in DB-treated ones. β-glucosidase activity showed a soil-dependent behavior, while the pattern of C source utilization suggested a change of soil microbial community structure after herbicide (especially DB) spiking. At 30 DAS, the herbicides’ impact on soil microorganisms, enzyme activity and functional diversity was still visible. Moreover, a toxic effect of DB (at 50× and 500×), but not IMZ, was recorded vs. Rhizobium sullae, the bacterial symbiont of Hedysarum coronarium. The obtained results indicated that IMZ and DB are poorly sorbed and highly desorbed by both soils. Moreover, at the tested concentrations, IMZ and DB can have short- and medium-term impacts on the microbial component and the related activity of the investigated soils, likely affecting a range of ecosystem services provided by soil microorganisms. Full article

(This article belongs to the Special Issue Advanced Research of Soil Microbial Functional Diversity)

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15 pages, 3776 KiB

Open AccessArticle

Effects of Nitrogen Addition on Soil Microbial Functional Diversity and Extracellular Enzyme Activities in Greenhouse Cucumber Cultivation

by Zhen Wang, Shuang Wang, Ting Bian, Qiaobo Song, Guorui Wu, Muhammad Awais, Yufeng Liu, Hongdan Fu and Zhouping Sun

Agriculture 2022, 12(9), 1366; https://doi.org/10.3390/agriculture12091366 - 01 Sep 2022

Cited by 3 | Viewed by 1830

Abstract

Greenhouses, commonly used for vegetable production, are experiencing large nitrogen (N) inputs in North China, which leads to soil acidification, increases soil N availability, and affects microbial community structure and composition. However, it remains unclear how N enrichment influences soil microbial functional activities [...] Read more.

Greenhouses, commonly used for vegetable production, are experiencing large nitrogen (N) inputs in North China, which leads to soil acidification, increases soil N availability, and affects microbial community structure and composition. However, it remains unclear how N enrichment influences soil microbial functional activities in this region. In this study, we conducted a two-year pot experiment in a greenhouse to evaluate the effects of four different rates of N addition (0, 334, 668, and 1002 kg N ha⁻¹ year⁻¹) on cucumber soil properties, extracellular enzyme activities, and community level physiological profiles (CLPP). We found that high-N addition (1002 kg N ha⁻¹) caused a massive accumulation of inorganic nitrogen and soil acidification, which was not beneficial to soil microbial activities. The color development (AWCD) values for the metabolism of microbial carbon sources and the activities of soil extracellular enzymes also showed a significant decrease in high N(N3) treatment. Additionally, the activity of leucine aminopeptidase (LAP) and polyphenol oxidase (PPO) of N3 decreased by 36% and 50% compared to the N0 and could be a good predictor for microbial functional diversity and microbial biomass carbon (MBC). Structural equation modeling (SEM) confirmed that the reduction of microbial functional diversity is mainly coregulated by the decline of soil pH and the change of cucumber BGB (belowground biomass) resulting from soil C and N imbalance. Overall, excessive N-fertilizer amendment can be more dangerous to microbial community functional diversity, especially for carbohydrate utilization which adversely affects cucumber yield in current intensive management. Full article

(This article belongs to the Special Issue Advanced Research of Soil Microbial Functional Diversity)

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22 pages, 4197 KiB

Open AccessEditor’s ChoiceArticle

N₂O Emission and Nitrification/Denitrification Bacterial Communities in Upland Black Soil under Combined Effects of Early and Immediate Moisture

by Lei Wang, Da-Cheng Hao, Sisi Fan, Hongtu Xie, Xuelian Bao, Zhongjun Jia and Lianfeng Wang

Agriculture 2022, 12(3), 330; https://doi.org/10.3390/agriculture12030330 - 25 Feb 2022

Cited by 10 | Viewed by 3343

Abstract

Soil moisture is the major factor influencing microbial properties and nitrous oxide (N₂O) production. Agricultural soils can be probed under wetting, wet/dry alternating, and constant moisture conditions to evaluate the combined effects of early (previous) and immediate (current) moisture on N [...] Read more.

Soil moisture is the major factor influencing microbial properties and nitrous oxide (N₂O) production. Agricultural soils can be probed under wetting, wet/dry alternating, and constant moisture conditions to evaluate the combined effects of early (previous) and immediate (current) moisture on N₂O emission and nitrification/denitrification. In view of the water history of upland black soil, five moisture regimes comprising different antecedent and present water holding capacity (WHC) levels were set up in the microcosm study. The 20% WHC was adopted as the initial legacy moisture, while three immediate water statuses include constant WHC, dry-wet cycle, and incremental moisture. Quantitative PCR and 16S rRNA amplicon sequencing were used to assess the impact of current and previous moisture on the bacterial community composition and abundance of nitrification/denitrification genes (amoA, nirS, and nosZ); the soil physicochemical properties, and N₂O emission were monitored. The N₂O production and nitrifying-denitrifying microbial communities were influenced by the antecedent moisture and pattern of the dry-wet cycle. The nitrifying-denitrifying microbial communities, especially members of β-/γ-Proteobacteria, Bacteroidetes and Gemmatimonadetes, in black soil were important in explaining the variation of N₂O production. The key taxonomic groups in response to the moisture alteration, e.g., Acidobacteria, Sphingobacteriia, Deltaproteobacteria, Methylobacterium, Gemmatimonas and Pseudarthrobacter, etc., were also highlighted. The soil nitrate, ammonium nitrogen, N₂O emission, nitrification/denitrification and mineralization were profoundly impacted by water regimes and showed statistically significant correlation with specific bacterial genera; the nitrite/nitrate reduction to ammonium could be boosted by high moisture. Both nitrifier denitrification and heterotrophic denitrification could be enhanced substantially when the black soil moisture was increased to above 60% WHC. These findings help evaluate the effects of the water mode on the N₂O emission from black soil, as well as the associated impacts on both soil fertility and the global environment. Full article

(This article belongs to the Special Issue Advanced Research of Soil Microbial Functional Diversity)

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27 pages, 3370 KiB

Open AccessArticle

Short-Term Resilience of Soil Microbial Communities and Functions Following Severe Environmental Changes

by Stefano Mocali, Antonio Gelsomino, Paolo Nannipieri, Roberta Pastorelli, Laura Giagnoni, Beatrix Petrovicova and Giancarlo Renella

Agriculture 2022, 12(2), 268; https://doi.org/10.3390/agriculture12020268 - 14 Feb 2022

Cited by 4 | Viewed by 2529

Abstract

Soil microorganisms are key drivers of soil biochemical processes, but the resilience of microbial communities and their metabolic activity after an extreme environmental change is still largely unknown. We studied structural (bacterial and fungal communities) and functional responses (soil respiration, adenosine triphosphate (ATP) [...] Read more.

Soil microorganisms are key drivers of soil biochemical processes, but the resilience of microbial communities and their metabolic activity after an extreme environmental change is still largely unknown. We studied structural (bacterial and fungal communities) and functional responses (soil respiration, adenosine triphosphate (ATP) content, hydrolase activities involved in the mineralization of organic C, N, P and S, and microbial community-level physiological profiles (CLPPs)) during the microbial recolonization of three heat-sterilized forest soils followed by cross- or self-reinoculation and incubation for 1, 7 and 30 days. Soil ATP content, biochemical activities and CLPP were annihilated by autoclaving, whereas most of the hydrolase activities were reduced to varying extents depending on the soil and enzyme activity considered. During the incubation period, the combination of self- and cross-reinoculation of different sterilized soils produced rapid dynamic changes in enzymatic activity as well as in microbial structure and catabolic activity. Physicochemical properties of the original soils exerted a major influence in shaping soil functional diversity, while reinoculation of sterilized soils promoted faster and greater changes in bacterial community structure than in fungal communities, varying with incubation period and soil type. Our results also confirmed the importance of microbial richness in determining soil resilience under severe disturbances. In particular, the new microbial communities detected in the treated soils revealed the occurrence of taxa which were not detected in the original soils. This result confirmed that rare microbial taxa rather than the dominant ones may be the major drivers of soil functionality and resilience. Full article

(This article belongs to the Special Issue Advanced Research of Soil Microbial Functional Diversity)

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15 pages, 2468 KiB

Open AccessArticle

Comparative Analysis of Arbuscular Mycorrhizal Fungal Communities between Farmland and Woodland in the Black Soil Region of Northeast China

by Wenying Yang, Mengjie Zhang, Fengbin Song, Shengqun Liu, Xiangnan Li and Xiancan Zhu

Agriculture 2021, 11(9), 866; https://doi.org/10.3390/agriculture11090866 - 10 Sep 2021

Cited by 4 | Viewed by 2350

Abstract

The black soil region of northeast China is a critical production base for commercial grain in China. Arbuscular mycorrhizal fungi (AMF) are widely present in terrestrial ecosystems and play a vital role in ecosystem stability. Here, we investigated the diversity and composition of [...] Read more.

The black soil region of northeast China is a critical production base for commercial grain in China. Arbuscular mycorrhizal fungi (AMF) are widely present in terrestrial ecosystems and play a vital role in ecosystem stability. Here, we investigated the diversity and composition of AMF communities in farmland and woodland from 20 sites in the black soil region of northeast China using Illumina MiSeq sequencing. The sequences were classified into 1 phylum, 1 class, 4 orders, 8 families, and 11 genera. Glomerales and Paraglomerales were observed as the most abundant order in farmland and woodland, respectively, and also belonged to abundant orders of the black soil region in northeast China, accounting for more than 90% of the total. Furthermore, Paraglomus, Claroideoglomus, and Glomus were the most abundant genera. Canonical correspondence analysis demonstrated the effect of soil pH, invertase, nitrogen, phosphorus, and soil organic carbon (SOC) contents on AMF community composition. Results from the correlation analysis revealed a reduction in AMF diversity with increases in SOC and phosphorus contents. These findings suggest AMF community composition varied with land use type (farmland and woodland), and provide a basis for protecting and utilizing AMF resources in the black soil region of northeast China. Full article

(This article belongs to the Special Issue Advanced Research of Soil Microbial Functional Diversity)

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12 pages, 1354 KiB

Open AccessArticle

Pseudomonas putida Isolation and Quantification by Real-Time PCR in Agricultural Soil Biodegradable Mulching

by Stefania Fontanazza, Alessia Restuccia, Giovanni Mauromicale, Aurelio Scavo and Cristina Abbate

Agriculture 2021, 11(8), 782; https://doi.org/10.3390/agriculture11080782 - 17 Aug 2021

Cited by 9 | Viewed by 3985

Abstract

To reduce the plastic waste problem in agriculture, biodegradable plastic (BP) mulch films have become of key importance thanks to their biodegradability and beneficial effects on crops. However, at present, BPs cannot always replace conventional plastics, because biodegradation is governed by many biotic [...] Read more.

To reduce the plastic waste problem in agriculture, biodegradable plastic (BP) mulch films have become of key importance thanks to their biodegradability and beneficial effects on crops. However, at present, BPs cannot always replace conventional plastics, because biodegradation is governed by many biotic and abiotic factors under field conditions. This research aimed at isolating and identifying, from soil particles directly attached to the surface of BP samples, the microorganisms responsible of degradation through a combined approach based on biodegradation and molecular tests. For this purpose, a field trial within a Mediterranean apricot orchard was carried out to study the biodegradation of a commercial BP mulch with respect to a no-BP, a conventional apricot management, following the standard agricultural practices, and a subterranean clover cover cropping, either incorporating or leaving its dead mulches on the soil surface. After BP film appeared visibly degraded in field, we isolated from soil particles attached to the polymer surface, a mesophilic bacterium with certain degradative potential assessed by plate and liquid assays, identified by sequencing as Pseudomonas putida. Quantitative real time PCR analysis showed the P. putida was significantly more abundant in PB plots than the other plot treatments. These preliminary results are potentially applicable to accelerate the degradation of BP mulch films and decrease the plastic pollution in agriculture. Full article

(This article belongs to the Special Issue Advanced Research of Soil Microbial Functional Diversity)

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15 pages, 1991 KiB

Open AccessEditor’s ChoiceArticle

Effects of Short-Term Rice Straw Return on the Soil Microbial Community

by Enze Wang, Xiaolong Lin, Lei Tian, Xinguang Wang, Li Ji, Feng Jin and Chunjie Tian

Agriculture 2021, 11(6), 561; https://doi.org/10.3390/agriculture11060561 - 18 Jun 2021

Cited by 16 | Viewed by 4340

Abstract

Rice straw is a byproduct of agricultural production and an important agricultural resource. However, rice straw has not yet been effectively used, and incorrect treatment methods (such as burning in the field) can cause serious damage to the environment. Studies have shown that [...] Read more.

Rice straw is a byproduct of agricultural production and an important agricultural resource. However, rice straw has not yet been effectively used, and incorrect treatment methods (such as burning in the field) can cause serious damage to the environment. Studies have shown that straw returning is beneficial to soil, but there have been few studies focused on the effect of the amount of short-term straw returned on the soil microbial community. This study evaluates 0%, 50%, 75%, and 100% rice straw returned to the field on whether returning different amounts of straw in the short term would affect the diversity and composition of the soil microbial community and the correlation between bacteria and fungi. The results show that the amount of straw returned to the field is the main factor that triggers the changes in the abundance and composition of the microbial community in the paddy soil. A small amount of added straw (≤50% straw added) mainly affects the composition of the bacterial community, while a larger amount of added straw (>50% straw added) mainly affects the composition of the fungal community. Returning a large amount of straw increases the microbial abundance related to carbon and iron cycles in the paddy soil, thus promoting the carbon and iron cycle processes to a certain extent. In addition, network analysis shows that returning a large amount of straw also increases the complexity of the microbial network, which may encourage more microbes to be niche-sharing and comprehensively improve the ecological environment of paddy soil. This study may provide some useful guidance for rice straw returning in northeast China. Full article

(This article belongs to the Special Issue Advanced Research of Soil Microbial Functional Diversity)

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18 pages, 9552 KiB

Open AccessArticle

The Effects of Microbial Inoculants on Bacterial Communities of the Rhizosphere Soil of Maize

by Minchong Shen, Jiangang Li, Yuanhua Dong, Zhengkun Zhang, Yu Zhao, Qiyun Li, Keke Dang, Junwei Peng and Hong Liu

Agriculture 2021, 11(5), 389; https://doi.org/10.3390/agriculture11050389 - 25 Apr 2021

Cited by 5 | Viewed by 2810

Abstract

The bacterial community of rhizosphere soil maintains soil properties, regulates the microbiome, improves productivity, and sustains agriculture. However, the structure and function of bacterial communities have been interrupted or destroyed by unreasonable agricultural practices, especially the excessive use of chemical fertilizers. Microbial inoculants, [...] Read more.

The bacterial community of rhizosphere soil maintains soil properties, regulates the microbiome, improves productivity, and sustains agriculture. However, the structure and function of bacterial communities have been interrupted or destroyed by unreasonable agricultural practices, especially the excessive use of chemical fertilizers. Microbial inoculants, regarded as harmless, effective, and environmentally friendly amendments, are receiving more attention. Herein, the effects of three microbial inoculants, inoculant M and two commercial inoculants (A and S), on bacterial communities of maize rhizosphere soil under three nitrogen application rates were compared. Bacterial communities treated with the inoculants were different from those of the non-inoculant control. The OTU (operational taxonomic unit) numbers and alpha diversity indices were decreased by three inoculants, except for the application of inoculant M in CF group. Beta diversity showed the different structures of bacterial communities changed by three inoculants compared with control. Furthermore, key phylotypes analyses exhibited the differences of biomarkers between different treatments visually. Overall, inoculant M had shared and unique abilities of regulating bacterial communities compared with the other two inoculants by increasing potentially beneficial bacteria and decreasing the negative. This work provides a theoretical basis for the application of microbial inoculants in sustainable agriculture. Full article

(This article belongs to the Special Issue Advanced Research of Soil Microbial Functional Diversity)

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18 pages, 2877 KiB

Open AccessEditor’s ChoiceArticle

Plant Growth-Promoting Rhizobacteria Isolated from the Jujube (Ziziphus lotus) Plant Enhance Wheat Growth, Zn Uptake, and Heavy Metal Tolerance

by Nidal Fahsi, Ismail Mahdi, Abdelhalem Mesfioui, Latefa Biskri and Abdelmounaaim Allaoui

Agriculture 2021, 11(4), 316; https://doi.org/10.3390/agriculture11040316 - 04 Apr 2021

Cited by 44 | Viewed by 5362

Abstract

In recent years, the low Zn content of wheat has become critical. Consequently, solutions that can improve the Zn nutrition of wheat are highly researched. In the present investigation, we aimed to evaluate the potential benefits of phosphate-solubilizing bacteria isolated from Ziziphus lotus [...] Read more.

In recent years, the low Zn content of wheat has become critical. Consequently, solutions that can improve the Zn nutrition of wheat are highly researched. In the present investigation, we aimed to evaluate the potential benefits of phosphate-solubilizing bacteria isolated from Ziziphus lotus on wheat seedling growth. Based on the phosphate-solubilizing criteria, four isolated strains, J16, J143, J146, and J158, were identified by 16SrRNA gene sequencing as Pseudomonas moraviensis, Bacillus halotolerans, Enterobacter hormaechei, and Pseudomonas frederiksbergensis, respectively. Studies of the conventional properties of plant growth-promoting rhizobacteria (PGPR) showed that E. hormaechei J146 produced up to 550 mg·L⁻¹ of indole-3-acetic acid (IAA). Siderophores and ammonia were produced by all strains but cellulase was restricted to B. halotolerans J143, whereas proteases were missing in E. hormaechei J146 and P. frederiksbergensis J158. E. hormaechei J146 tolerate up to 1.5 mg·L⁻¹ of copper and cadmium, while B. halotolerans J143 withstood 1.5 mg·L⁻¹ of nickel. Strains B. halotolerant J143, E. hormaechei J146, and P. frederiksbergensis J158 remarkably improved wheat seed germination, plant growth, and Zn absorption. Lastly, nutrient measurement revealed that a wheat plant inoculated with E. hormaechei J146 and P. frederiksbergensis J158 increased its nitrogen and potassium uptake by up to 17%. Full article

(This article belongs to the Special Issue Advanced Research of Soil Microbial Functional Diversity)

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22 pages, 3715 KiB

Open AccessArticle

Halotolerant Endophytic Bacterium Serratia rubidaea ED1 Enhances Phosphate Solubilization and Promotes Seed Germination

by Ismail Mahdi, Mohamed Hafidi, Abdelmounaaim Allaoui and Latefa Biskri

Agriculture 2021, 11(3), 224; https://doi.org/10.3390/agriculture11030224 - 09 Mar 2021

Cited by 11 | Viewed by 4095

Abstract

Quinoa is renowned for its nutritional value and ability to withstand harsh environmental conditions such as salinity. In the present work, we isolated 34 phosphate solubilizing endophytic bacteria associated with the roots of quinoa plants. Based on phosphate solubilization efficiency and biochemical characterization, [...] Read more.

Quinoa is renowned for its nutritional value and ability to withstand harsh environmental conditions such as salinity. In the present work, we isolated 34 phosphate solubilizing endophytic bacteria associated with the roots of quinoa plants. Based on phosphate solubilization efficiency and biochemical characterization, we selected one isolate named ED1. Ribotyping using partial 16S RNA gene analysis revealed that the selected isolate shares 99.7% identity with Serratia rubidaea. Plant growth promoting (PGP) studies showed that the ED1 strain solubilized complexed forms of phosphate (Ca₃(PO₄)₂). Zinc release from ZnO, Zn₃(PO₄)₂, or ZnCO₃ revealed the efficient ZnO solubilization by the ED1 strain. Except for proteases, the strain ED1 produced siderophores, cellulase, ammonia and exhibited oligonitrophilic features. Indole acetic acid (IAA) production was detected with and without the L-tryptophan precursor. Next, we demonstrated that the ED1 strain tolerated 1.5 M NaCl final concentration and exhibited intrinsic resistance to seven antibiotics frequently prescribed for medical use. Moreover, we found that ED1 strain withstood 2 mg/L of Cadmium and 1 mg/L of either Nickel or Copper. Furthermore, we observed that S. rubidaea ED1 stimulated quinoa seeds germination and seedlings growth under salt stress conditions. Lastly, we discuss the advantages versus disadvantages of applying the S. rubidaea ED1 strain as a beneficial agent for salty and/or heavy metals contaminated soils. Full article

(This article belongs to the Special Issue Advanced Research of Soil Microbial Functional Diversity)

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14 pages, 2831 KiB

Open AccessArticle

The Immense Functional Attributes of Maize Rhizosphere Microbiome: A Shotgun Sequencing Approach

by Saheed Adekunle Akinola, Ayansina Segun Ayangbenro and Olubukola Oluranti Babalola

Agriculture 2021, 11(2), 118; https://doi.org/10.3390/agriculture11020118 - 02 Feb 2021

Cited by 8 | Viewed by 3007

Abstract

The northwest (NW) province of South Africa is a semi-arid area, often disturbed by soil extremes such as drought and intense temperature. However, many functions possessed by the rhizosphere microbiome are still required, especially those inhabiting arid and semi-arid soils. This study involves [...] Read more.

The northwest (NW) province of South Africa is a semi-arid area, often disturbed by soil extremes such as drought and intense temperature. However, many functions possessed by the rhizosphere microbiome are still required, especially those inhabiting arid and semi-arid soils. This study involves a metagenomic comparison of the major metabolic attributes of two maize rhizosphere soils and their surrounding soils. Here, we hypothesized that there is a considerable difference between the functional diversity of maize rhizosphere and bulk soils and that the rhizosphere soil has distinct functional traits of agricultural importance. A high-throughput sequencing approach was used to assess the metabolic profile of rhizosphere soil microbiota of maize collected from the Gauteng and NW provinces of South Africa. The relative abundance of 13 functional hit categories was significantly different between the sampling sites. The diversity indices showed a considerable difference between the rhizosphere and surrounding soils. The difference in the chemical properties of the sampling sites was responsible for the variation in the microbial functional composition. Nevertheless, the presence of a high relative abundance of functional categories with unknown functions in SEED subsystem-2 coupled with the large number of functional hits conferring a response to soil stressors viz. oxidative stress, heat shock, osmotic stress, and cold shock noticed in the rhizosphere samples may indicate the presence of novel genes at the sampling sites. Exploring the plant growth-promoting traits of microorganisms present at these sites could eliminate the constraint posed by soil stressors on sustainable agriculture. Full article

(This article belongs to the Special Issue Advanced Research of Soil Microbial Functional Diversity)

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16 pages, 1012 KiB

Open AccessArticle

Functional Diversity of Soil Microbial Community after Conversion of a Chestnut Forest to an Agricultural System

by Paola Iovieno, Riccardo Scotti and Massimo Zaccardelli

Agriculture 2021, 11(1), 43; https://doi.org/10.3390/agriculture11010043 - 09 Jan 2021

Viewed by 2258

Abstract

In the National park of Cilento, Vallo di Diano and Alburni (South Italy), a portion of a chestnut forest was converted in 2012 into an agricultural system in order to crop a local variety of bean. We investigated the effect over time of [...] Read more.

In the National park of Cilento, Vallo di Diano and Alburni (South Italy), a portion of a chestnut forest was converted in 2012 into an agricultural system in order to crop a local variety of bean. We investigated the effect over time of the conversion on the functional diversity of the soil microbial community by two different approaches: the catabolic response profile, based on the short time CO₂ evolution induced by 25 simple organic substrates and the Biolog community level physiological profile (CLPP), based on the growth of microorganisms on 31 different substrates. The soils were sampled at 13, 17, 29, 41 and 49 months after the soil use change. The results showed that the soil use change did not produce evident modifications of the substrate utilization patterns, but rather a general decrease in the activity in the agricultural soils, as a consequence of the reduction in organic matter content. The results also showed seasonal effects on the substrate utilization profiles and on the calculated functional diversity indexes. The two approaches appeared to be complementary: Degens catabolic response profile was more able to discriminate between the two systems, whereas the Biolog was more able to highlight the variability among samplings. Full article

(This article belongs to the Special Issue Advanced Research of Soil Microbial Functional Diversity)

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30 pages, 4134 KiB

Open AccessEditor’s ChoiceReview

Soil Bioplastic Mulches for Agroecosystem Sustainability: A Comprehensive Review

by Cristina Abbate, Aurelio Scavo, Gaetano Roberto Pesce, Stefania Fontanazza, Alessia Restuccia and Giovanni Mauromicale

Agriculture 2023, 13(1), 197; https://doi.org/10.3390/agriculture13010197 - 12 Jan 2023

Cited by 10 | Viewed by 4672

Abstract

The use of plastic mulch films is widespread in agriculture for specialty cropping systems because of several benefits. In this article, we critically review, for the first time under a holistic approach, the use of biodegradable plastic mulches (BdPMs) in soil as a [...] Read more.

The use of plastic mulch films is widespread in agriculture for specialty cropping systems because of several benefits. In this article, we critically review, for the first time under a holistic approach, the use of biodegradable plastic mulches (BdPMs) in soil as a sustainable alternative to conventional petroleum-based plastics, highlighting the current state of understanding of their degradation in soil and their effect on soil microorganisms, weed control, and soil properties. In addition, we provide a detailed focus on the history and economic importance of mulching. BdPMs are effective for use in vegetable production in that they improve physical, chemical, and biological soil properties, as well as enhancing microbial biodiversity, controlling weeds, and maintaining soil moisture. BdPMs could be useful to limit the use of agrochemicals and reduce tillage and irrigation supplies for sustainable management. Full article

(This article belongs to the Special Issue Advanced Research of Soil Microbial Functional Diversity)

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