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Microorganisms
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BRICS Soil Microbiome
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BRICS Soil Microbiome

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

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 11534

Special Issue Editors

Prof. Dr. Yilai Lou

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Guest Editor
Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: soil micro-food web; soil nematode; soil microbiome; carbon cycling
Special Issues, Collections and Topics in MDPI journals
Dr. Liangshan Feng

E-Mail Website
Guest Editor
Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
Interests: drought-resistant agriculture, farming system, conservation tillage, soil amendment.
Special Issues, Collections and Topics in MDPI journals
Dr. Lucas William Mendes

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Guest Editor
Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Sao Paulo, Brazil
Interests: ecogenomics; microbial ecology; plant-microbes interaction; environmental microbiology; microbiomes; bioinformatics
Dr. Anna Gunina

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Guest Editor
Dokuchaev Soil Science Institute, Moscow, Russia
Interests: soil biology; plant-microbial interactions; rhizosphere; C, N, P cycling in soil
Dr. Wen Xing

E-Mail Website
Guest Editor
Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: soil microbiome; nematode; soil micro-food web

Special Issue Information

Dear Colleagues,

During the 2022 BRICS conference, the five BRICS countries of Brazil, Russia, India, China, and South Africa focused together on sustainable development of agriculture. Soil microbiome, including bacteria, fungi, archaea, virus, protist, and microfauna, plays key roles in underpinning ecosystem functions such as carbon and nitrogen cycling and in delivering ecosystem services including food security and climate mitigation. This is normally crucial for sustaining agriculture, and the quick advancements in molecular techniques and bioinformatics have greatly boosted soil microbiome research. However, we are still constrained in our knowledge of ecological processes and relevant mechanisms of soil microbiome in mediating element cycling, in remedying soil pollution, and in controlling soil-borne disease. This Special Issue focusing on the latest advances in soil microbiome in BRICS countries aims to promote scholarly communications among BRICS countries and to share relevant research achievements with the world. This will be significant for informing soil microbiome regulation for worldwide sustainable agriculture.

In this Special Issue, original research articles and reviews only from BRICS countries are welcome. Research areas may include (but are not limited to) the following:

  • Soil microbiome mediating element cycling
  • Microbiome linking to soil multifunctionality and function stability
  • Microbiome for soil pollution remediation
  • Microbiome in relation to soil-borne disease control and plant defense
  • Stress-resistant microbiota and degraded soil restoration

We look forward to receiving your contributions.

Prof. Dr. Yilai Lou
Dr. Liangshan Feng
Dr. Lucas William Mendes
Dr. Anna Gunina
Dr. Wen Xing
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • soil microbiome
  • soil microbiota
  • microorganism
  • protist
  • virus
  • nematode

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Published Papers (5 papers)

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Research

11 pages, 2130 KiB  
Article
Examining the Shift in the Decomposition Channel Structure of the Soil Decomposer Food Web: A Methods Comparison
by Wen Xing, Ning Hu, Zhongfang Li, Meng Yuan, Meiling Luo, Shuo Han, Evgenia Blagodatskaya, Shunbao Lu and Yilai Lou
Microorganisms 2023, 11(10), 2589; https://doi.org/10.3390/microorganisms11102589 - 19 Oct 2023
Cited by 1 | Viewed by 1212
Abstract
Selecting the appropriate indicators and measuring time point numbers is important for accurately examining the shift in soil gross decomposition channel structure. Through a selected case study on a natural forest vs. rainfed arable system over a two-month-long experiment, the utility of three [...] Read more.
Selecting the appropriate indicators and measuring time point numbers is important for accurately examining the shift in soil gross decomposition channel structure. Through a selected case study on a natural forest vs. rainfed arable system over a two-month-long experiment, the utility of three commonly employed indicators (fungi to bacteria ratio (F:B), fungivore to bacterivore ratio (FF:BF), and glucosamine to muramic acid ratio (GlcN:MurN)) were compared to reflect the shift in soil gross decomposition channel structure. The requirement of measuring the time point numbers for the three indicators was also assessed, and we suggest a potential methodology. Our results revealed that the GlcN:MurN ratio was more reliable for assessing the shifts in gross decomposition channel structure for long-term land use changes, while it was less sensitive to short-term drought compared with the other two indicators. The F:B ratio was more applicable than the FF:BF ratio for reflecting both long- and short-term changes. Furthermore, the reliability of the GlcN:MurN ratio was the least dependent on measuring time point numbers. We suggest the use of multiple indicators and the adoption of multiple measuring time points for the overall methodology. Full article
(This article belongs to the Special Issue BRICS Soil Microbiome)
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15 pages, 1182 KiB  
Article
West-Siberian Chernozem: How Vegetation and Tillage Shape Its Bacteriobiome
by Natalia Naumova, Pavel Barsukov, Olga Baturina, Olga Rusalimova and Marsel Kabilov
Microorganisms 2023, 11(10), 2431; https://doi.org/10.3390/microorganisms11102431 - 28 Sep 2023
Cited by 1 | Viewed by 936
Abstract
Managing soil biodiversity using reduced tillage is a popular approach, yet soil bacteriobiomes in the agroecosystems of Siberia has been scarcely studied, especially as they are related to tillage. We studied bacteriobiomes in Chernozem under natural steppe vegetation and cropped for wheat using [...] Read more.
Managing soil biodiversity using reduced tillage is a popular approach, yet soil bacteriobiomes in the agroecosystems of Siberia has been scarcely studied, especially as they are related to tillage. We studied bacteriobiomes in Chernozem under natural steppe vegetation and cropped for wheat using conventional or no tillage in a long-term field trial in the Novosibirsk region, Russia, by using the sequence diversity of the V3/V4 region of 16S rRNA genes. Actinobacteria, Acidobacteria, and Proteobacteria summarily accounted for 80% of the total number of sequences, with Actinobacteria alone averaging 51%. The vegetation (natural vs. crop) and tillage (ploughed vs. no-till) affected the bacterial relative abundance at all taxonomic levels and many taxa, e.g., hundreds of OTUs. However, such changes did not translate into α-biodiversity changes, i.e., observed and potential OTUs’ richness, Shannon, and Simpson, excepting the slightly higher evenness and equitability in the top 0–5 cm of the undisturbed soil. As for the β-biodiversity, substituting conventional ploughing with no tillage and maintaining the latter for 12 years notably shifted the soil bacteriobiome closer to the one in the undisturbed soil. This study, presenting the first inventory of soil bacteriobiomes under different tillage in the south of West Siberia, underscores the need to investigate the seasonality and longevity aspects of tillage, especially as they are related to crop production. Full article
(This article belongs to the Special Issue BRICS Soil Microbiome)
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15 pages, 3594 KiB  
Article
Bacterial Community Composition and Isolation of Actinobacteria from the Soil of Flaming Mountain in Xinjiang, China
by Zixuan He, Yuxian Wang, Xiaoyu Bai, Min Chu, Yuanyang Yi, Jing Zhu, Meiying Gu, Ling Jiang and Zhidong Zhang
Microorganisms 2023, 11(2), 489; https://doi.org/10.3390/microorganisms11020489 - 16 Feb 2023
Cited by 4 | Viewed by 2465
Abstract
In this work, bacterial community composition and actinobacteria resources were explored in extremely hot and hyper-arid areas of Flaming Mountain. This was achieved through a combination of PCR amplicon sequencing of bacterial 16S rRNA gene and cultivation-dependent isolation and characterization efforts. According to [...] Read more.
In this work, bacterial community composition and actinobacteria resources were explored in extremely hot and hyper-arid areas of Flaming Mountain. This was achieved through a combination of PCR amplicon sequencing of bacterial 16S rRNA gene and cultivation-dependent isolation and characterization efforts. According to the high-throughput sequencing results and soil characteristics, 11 kinds of media were firstly designed to isolate actinobacteria, following the screening and identification of related strains. The results showed that a total of 2994 operational taxonomic units (OTUs) were obtained, involving 22 phyla, 77 orders and 121 genera. Among them, actinobacteria with the relative abundance of 8% ranked third, accounting for 33 genera and 47 species. A total of 132 strains distributed by eight families and 11 genera of actinobacteria were isolated from 11 media, of which six strains were potential new species. Furthermore, the functional characteristics of isolated strains were preliminarily evaluated. The results showed that the obtained strains generally had tolerance against heat, salt and alkali. Fifty-two strains had antibacterial activity, 69 strains could produce hydrolases, and 12.4% of the strains had quorum sensing inhibitory activity. The present study has laid a solid foundation for further understanding the bacterial diversity and exploiting actinobacteria resources in the Flaming Mountain area. Full article
(This article belongs to the Special Issue BRICS Soil Microbiome)
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19 pages, 2602 KiB  
Article
Experimental Study on Silt Soil Improved by Microbial Solidification with the Use of Lignin
by Yongshuai Sun, Xinyan Zhong, Jianguo Lv and Guihe Wang
Microorganisms 2023, 11(2), 281; https://doi.org/10.3390/microorganisms11020281 - 20 Jan 2023
Cited by 3 | Viewed by 2275
Abstract
At present, in the field of geotechnical engineering and agricultural production, with increasingly serious pollution an environmentally friendly and efficient means is urgently needed to improve the soil mass. This paper mainly studied the microbial induced calcium carbonate precipitation (MICP) technology and the [...] Read more.
At present, in the field of geotechnical engineering and agricultural production, with increasingly serious pollution an environmentally friendly and efficient means is urgently needed to improve the soil mass. This paper mainly studied the microbial induced calcium carbonate precipitation (MICP) technology and the combined effect of MICP technology and lignin on the improvement of silt in the Beijing area. Through unconfined compressive strength and dynamic triaxial test methods, samples improved by microorganisms were studied to obtain the optimal values of cement concentration and lignin under these two test schemes. The results show that after the incubation time of Sporosarcina pasteurii reached 24 h, the OD600 value was 1.7–2.0 and the activity value (U) was 930–1000 mM ms/min. In the unconfined static pressure strength test, after MICP treatment the optimal concentration of cementitious solution for constant temperature and humidity samples and constant-temperature immersion samples was 1.25 mol/L. The compressive strength of the constant temperature and humidity sample was 1.73 MPa, and the compressive strength of the constant-temperature immersion sample was 3.62 Mpa. At the concentration of 1.25 mol/L of cement solution, MICP technology combined with lignin could improve the constant temperature and humidity silt sample. The optimal addition ratio of lignin was 4%, and its compressive strength was 1.9 MPa. The optimal lignin addition ratio of the sample soaked at a constant temperature was 3%, and the compressive strength was 4.84 MPa. In the dynamic triaxial multi-stage cyclic load test, the optimal concentration of cementation solution for the constant temperature and humidity sample after MICP treatment was 1.0 mol/L, and the failure was mainly inclined cracks. However, in the condition of joint improvement of MICP and lignin, the sample mainly had a drum-shaped deformation, the optimal lignin addition ratio was 4%, and the maximum axial load that the sample could bear was 306.08 N. When the axial dynamic load reached 300 N, the strain accumulation of the 4% group was only 2.3 mm. In this paper, lignin, an ecofriendly material, was introduced on the basis of MICP technology. According to the failure shape and relevant results of the sample, the addition of lignin was beneficial for the improvement of the compressive strength of the sample. Full article
(This article belongs to the Special Issue BRICS Soil Microbiome)
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15 pages, 6519 KiB  
Article
Effects of the Long-Term Continuous Cropping of Yongfeng Yam on the Bacterial Community and Function in the Rhizospheric Soil
by Jian Yao, Caiyun Wu, Linjuan Fan, Meihua Kang, Zirong Liu, Yuhui Huang, Xueliang Xu and Yingjuan Yao
Microorganisms 2023, 11(2), 274; https://doi.org/10.3390/microorganisms11020274 - 20 Jan 2023
Cited by 7 | Viewed by 3748
Abstract
Replant disease caused by continuous cropping commonly occurs in yam with consecutive monoculture. However, little is known about how the continuous cropping of yam affects the rhizospheric soil bacterial community structure. In this study, the effects of continuous cropping on rhizospheric soil characteristics, [...] Read more.
Replant disease caused by continuous cropping commonly occurs in yam with consecutive monoculture. However, little is known about how the continuous cropping of yam affects the rhizospheric soil bacterial community structure. In this study, the effects of continuous cropping on rhizospheric soil characteristics, bacterial diversity, and community structure were investigated in the Yongfeng yam fields under monoculture for 1, 5, 10, 15, and 20 years. Long-term monoculture caused soil acidification and increased the concentration of available potassium (AK) and available phosphorus (AP), and soil bacterial richness, but decreased the soil bacterial diversity. An exception was for the field under monoculture for 20 years as it showed the highest bacterial diversity. The relative abundance of beneficial bacteria, such as Proteobacteria, Actinobacteria, and Chloroflexi decreased while the relative abundance of harmful bacteria, including Gemmatimonadetes and Acidobacteria, increased with an extended continuous cultivation time. The networks varied among yams with different cultivation years and became complex with the increase in cultivation years. However, after time in monoculture, the bacterial network decreased gradually and existed stably. These changes in bacterial community composition and co-occurrence of networks may increase the potential risk of soil-borne disease and reduce the yield and quality of Yongfeng yam. Full article
(This article belongs to the Special Issue BRICS Soil Microbiome)
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