Microorganisms

Research

15 pages, 2544 KiB

Open AccessArticle

by Mingyu Wang, Wenmiao Pu, Shenzheng Wang, Xiannan Zeng, Xin Sui and Xin Wang

Microorganisms 2023, 11(12), 2950; https://doi.org/10.3390/microorganisms11122950 - 9 Dec 2023

Cited by 1 | Viewed by 1048

Soil bacteria are crucial components of terrestrial ecosystems, playing an important role in soil biogeochemical cycles. Although bacterial community diversity and composition are regulated by many abiotic and biotic factors, how soil physiochemical properties impact the soil bacteria community diversity and composition in [...] Read more.

Soil bacteria are crucial components of terrestrial ecosystems, playing an important role in soil biogeochemical cycles. Although bacterial community diversity and composition are regulated by many abiotic and biotic factors, how soil physiochemical properties impact the soil bacteria community diversity and composition in wetland ecosystems remains largely unknown. In this study, we used high-throughput sequencing technology to investigate the diversity and composition of a soil bacterial community, as well as used the structural equation modeling (SEM) method to investigate the relationships of the soil’s physicochemical properties (i.e., soil pH, soil organic carbon (SOC), total nitrogen (TN), ammonium nitrogen (NH₄⁺N), electrical conductivity (EC) and nitrate nitrogen (NO₃⁻N)), and soil bacterial community structures in three typical wetland sites in the Sanjiang Plain wetland. Our results showed that the soil physicochemical properties significantly changed the α and β-diversity of the soil bacteria communities, e.g., soil TN, NH₄⁺N, NO₃⁻N, and SOC were the main soil factors affecting the soil bacterial α-diversity. The soil TN and pH were the key soil factors affecting the soil bacterial community. Our results suggest that changes in soil pH indirectly affect soil bacterial communities by altering the soil nitrogenous nutrient content. Full article

(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System)

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21 pages, 3626 KiB

Open AccessArticle

Rhizoglomus variabile and Nanoglomus plukenetiae, Native to Peru, Promote Coffee Growth in Western Amazonia

by Mike Anderson Corazon-Guivin, Gabriel Romero-Cachique, Karen M. Del Aguila, Amner Padilla-Domínguez, Angel David Hernández-Amasifuen, Agustin Cerna-Mendoza, Danny Coyne and Fritz Oehl

Microorganisms 2023, 11(12), 2883; https://doi.org/10.3390/microorganisms11122883 - 29 Nov 2023

Viewed by 959

Abstract

Coffee (Coffea arabica) is among the world’s most economically important crops. Coffee was shown to be highly dependent on arbuscular mycorrhizal fungi (AMF) in traditionally managed coffee plantations in the tropics. The objective of this study was to assess AMF species [...] Read more.

Coffee (Coffea arabica) is among the world’s most economically important crops. Coffee was shown to be highly dependent on arbuscular mycorrhizal fungi (AMF) in traditionally managed coffee plantations in the tropics. The objective of this study was to assess AMF species richness in coffee plantations of four provinces in Perú, to isolate AMF isolates native to these provinces, and to test the effects of selected indigenous AMF strains on coffee growth. AMF species were identified by morphological tools on the genus level, and if possible further to the species level. Two native species, Rhizoglomus variabile and Nanoglomus plukenetiae, recently described from the Peruvian mountain ranges, were successfully cultured in the greenhouse on host plants. In two independent experiments, both species were assessed for their ability to colonize coffee seedlings and improve coffee growth over 135 days. A total of 35 AMF morphospecies were identified from 12 plantations. The two inoculated species effectively colonized coffee roots, which resulted in 3.0–8.6 times higher shoot, root and total biomass, when compared to the non-mycorrhizal controls. R. variabile was superior to N. plukenetiae in all measured parameters, increasing shoot, root, and total biomass dry weight by 4.7, 8.6 and 5.5 times, respectively. The dual inoculation of both species, however, did not further improve plant growth, when compared to single-species inoculations. The colonization of coffee by either R. variabile or N. plukenetiae strongly enhances coffee plant growth. R. variabile, in particular, offers enormous potential for improving coffee establishment and productivity. Assessment of further AMF species, including species from other AMF families should be considered for optimization of coffee growth promotion, both alone and in combination with R. variabile. Full article

(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System)

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22 pages, 6057 KiB

Open AccessArticle

Enhancing Biocrust Development and Plant Growth through Inoculation of Desiccation-Tolerant Cyanobacteria in Different Textured Soils

by Priya Yadav, Rahul Prasad Singh, Abeer Hashem, Elsayed Fathi Abd_Allah, Gustavo Santoyo, Ajay Kumar and Rajan Kumar Gupta

Microorganisms 2023, 11(10), 2507; https://doi.org/10.3390/microorganisms11102507 - 7 Oct 2023

Cited by 1 | Viewed by 1546

Abstract

In recent years, there has been a burgeoning interest in the utilization of cyanobacteria for the purpose of land rehabilitation via enhancements in soil fertility, prevent erosion, and counter desertification. This study evaluated the ability of Nostoc calcicola BOT1, Scytonema sp. BOT2, and [...] Read more.

In recent years, there has been a burgeoning interest in the utilization of cyanobacteria for the purpose of land rehabilitation via enhancements in soil fertility, prevent erosion, and counter desertification. This study evaluated the ability of Nostoc calcicola BOT1, Scytonema sp. BOT2, and their consortia to form biocrusts on the substrate of coarse sand, fine sand, and loamy soil. A nutrient- and water-deficient substrate was inoculated with cyanobacteria to facilitate biocrust formation and evaluate their impact on agriculture. Cyanobacteria inoculation resulted in significant improvements in soil fertility, especially in coarse and fine sand, which initially had the lowest fertility. The findings of this investigation underscore that the consortium of cyanobacteria exhibited greater efficacy than individual strains in enhancing soil fertility and stimulating plant growth. The loamy soil treated with the consortium had the highest plant growth across all soil types, in contrast to the individual strains. The consortium of cyanobacteria showed promising results in promoting biocrust formation and fostering rice seedling growth in fine sand. This study provides empirical evidence supporting the potential utility of cyanobacterial consortia as a valuable tool for the rehabilitation of degraded land. Furthermore, the results indicate that cyanobacterial species can persist in soil environments even following prolonged periods of desiccation. Full article

(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System)

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19 pages, 4040 KiB

Open AccessArticle

Characterization of a Novel Bacillus glycinifermentans Strain MGMM1 Based on Full Genome Analysis and Phenotypic Properties for Biotechnological Applications

by Daniel Mawuena Afordoanyi, Roderic Gilles Claret Diabankana, Ernest Nailevich Komissarov, Evgenii Sergeyevich Kuchaev and Shamil Zavdatovich Validov

Microorganisms 2023, 11(6), 1410; https://doi.org/10.3390/microorganisms11061410 - 26 May 2023

Cited by 1 | Viewed by 1866

Abstract

Bacillus species have gained much attention based on their phenotypic characteristics and their genetic architecture as biological control agents and plant growth-promotor with bioremediation potential. In this study, we analyzed the whole genome of a novel strain, Bacillus glycinifermentans MGMM1, isolated from the [...] Read more.

Bacillus species have gained much attention based on their phenotypic characteristics and their genetic architecture as biological control agents and plant growth-promotor with bioremediation potential. In this study, we analyzed the whole genome of a novel strain, Bacillus glycinifermentans MGMM1, isolated from the rhizosphere of a weed plant (Senna occidentalis) and assayed its phenotypic characteristics, as well as antifungal and biocontrol ability. The whole genome analysis of MGMM1 identified 4259 putative coding sequences, with an encoding density of 95.75% attributed to biological functions, including genes involved in stimulating plant growth, such as acetolactate synthase, alsS, and genes involved in the resistance to heavy metal antimony (arsB and arsC). AntiSMASH revealed the presence of biosynthetic gene clusters plipastatin, fengycin, laterocidine, geobacillin II, lichenysin, butirosin A and schizokinen. Tests in vitro confirmed that MGMM1 exhibited antifungal activity against Fusarium oxysporum f.sp. radicis-lycopersici (Forl) ZUM2407, Alternaria alternata, F. graminearum and F. spp. and produce protease, lipase amylase and cellulase. Bacillus glycinifermentans MGMM1 demonstrated proteolytic (4.82 ± 1.04 U/mL), amylolytic (0.84 ± 0.05 U/mL) and cellulosic (0.35 ± 0.02 U/mL) enzymatic activities, as well as indole-3-acetic acid production (48.96 ± 1.43 μg/mL). Moreover, the probiotic strain MGMM1 demonstrated a high biocontrol potential of inhibiting (up to 51.45 ± 8.08%) the development of tomato disease caused by Forl ZUM2407. These results suggest that B. glycinifermentans MGMM1 has significant potential as a biocontrol, plant growth-promoting agent in agriculture. Full article

(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System)

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11 pages, 1994 KiB

Open AccessArticle

Colletotrichum siamense Strain LVY 9 Causing Spot Anthracnose on Winterberry Holly in China

by Lin Feng, Yahui Zhang, Weiliang Chen and Bizeng Mao

Microorganisms 2023, 11(4), 976; https://doi.org/10.3390/microorganisms11040976 - 9 Apr 2023

Cited by 2 | Viewed by 1465

Abstract

Winterberry holly (Ilex verticillata) is an economically valuable landscaping ornamental plant. Serious outbreaks have been reported, in its leaf tips curl upward, irregular black brown spots appear on leaves, and extensive defoliation is commonly observed. The incidence in Hangzhou was estimated [...] Read more.

Winterberry holly (Ilex verticillata) is an economically valuable landscaping ornamental plant. Serious outbreaks have been reported, in its leaf tips curl upward, irregular black brown spots appear on leaves, and extensive defoliation is commonly observed. The incidence in Hangzhou was estimated at 50% and resulted in large economic losses for growers in 2018. Samples were collected from the main cultivation area in Zhejiang Province. In total, 11 fungal isolates were obtained from diseased leaves through a single-spore purification method, and isolate LVY 9 exhibited strong pathogenicity. Based on morphology and molecular phylogenetic analyses based on multilocus sequence typing of the glyceraldehyde-3-phosphate dehydrogenase (GAPDH), internal transcribed spacer (ITS) regions, actin (ACT), calmodulin (CAL), and chitin synthase (CHS-1) genes, we identified the pathogen as Colletotrichum siamense, causative agent of anthracnose of winterberry holly. Full article

(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System)

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18 pages, 2876 KiB

Open AccessArticle

Meta-Analysis of the Effects of Biochar Application on the Diversity of Soil Bacteria and Fungi

by Mingyu Wang, Xiaoying Yu, Xiaohong Weng, Xiannan Zeng, Mengsha Li and Xin Sui

Microorganisms 2023, 11(3), 641; https://doi.org/10.3390/microorganisms11030641 - 2 Mar 2023

Cited by 7 | Viewed by 2070

Abstract

Biochar is increasingly being used for soil improvement, but the effects on microbial diversity in soil are still ambiguous due to contrasting results reported in the literature. We conducted a meta-analysis to clarify the effect of biochar addition on soil bacterial and fungal [...] Read more.

Biochar is increasingly being used for soil improvement, but the effects on microbial diversity in soil are still ambiguous due to contrasting results reported in the literature. We conducted a meta-analysis to clarify the effect of biochar addition on soil bacterial and fungal diversity with an increase in Shannon or Chao1 index as the outcome. Different experimental setups, quantitative levels of biochar addition, various biochar source materials and preparation temperatures, and the effect of natural precipitation in field experiments were the investigated variables. From a total of 95 publications identified for analysis, 384 datasets for Shannon index and 277 datasets for Chao1 index were extracted that described the bacterial diversity in the soils, of which field experiments and locations in China dominated. The application of biochar in soil significantly increased the diversity of soil bacteria but it had no significant effect on the diversity of fungi. Of the different experimental setups, the largest increase in bacterial diversity was seen for field experiments, followed by pot experiments, but laboratory and greenhouse settings did not report a significant increase. In field experiments, natural precipitation had a strong effect, and biochar increased bacterial diversity most in humid conditions (mean annual precipitation, MAP > 800 mm), followed by semi-arid conditions (MAP 200–400 mm). Biochar prepared from herbaceous materials was more effective to increase bacterial diversity than other raw materials and the optimal pyrolysis temperature was 350–550 °C. Addition of biochar at various levels produced inconclusive data for Chao1 and Shannon indices, and its effect was less strong than that of the other assessed variables. Full article

(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System)

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22 pages, 3420 KiB

Open AccessArticle

Fungicolous Fungi on Pseudosclerotial Plates and Apothecia of Hymenoscyphus fraxineus and Their Biocontrol Potential

by Tadeusz Kowalski and Piotr Bilański

Microorganisms 2022, 10(11), 2250; https://doi.org/10.3390/microorganisms10112250 - 14 Nov 2022

Cited by 1 | Viewed by 1864

Abstract

In the present work, research tasks were carried out in the search for fungi with potential biocontrol possibilities in relation to the ash dieback pathogen, Hymenoscyphus fraxineus. In the years 2012–2021, dead petioles of F. excelsior and F. mandshurica were collected, on [...] Read more.

In the present work, research tasks were carried out in the search for fungi with potential biocontrol possibilities in relation to the ash dieback pathogen, Hymenoscyphus fraxineus. In the years 2012–2021, dead petioles of F. excelsior and F. mandshurica were collected, on which morphological structures of H. fraxineus showed unusual symptoms of dying (apothecia) and signs of colonization by other fungi (pseudosclerotial plates). Based on morphological and molecular phylogenetic data, 18 fungal taxa were identified. Thirteen of them belong to Ascomycota: Clonostachys rosea, Cl. solani, Cordyceps sp., Minimidochium sp., Nemania diffusa, Fusarium sp., Pestalotiopsis sp., Trichoderma atroviride, T. harzianum, T. polysporum, T. rodmanii, T. tomentosum, Trichoderma sp., and five other taxa are represented by Basidiomycota: Corticiales sp., Cyathus olla, Efibula sp., Gymnopus sp. and Polyporales sp. In 108 dual cultures in vitro, three different types of interactions were distinguished: (i) physical colony contact (5.6%), (ii) presence of an inhibition zone between the colonies (0.9%), and (iii) copartner overgrowth of H. fraxineus colonies and partial or complete replacement of the pathogen (93.5%). In the dual cultures, various morphological deformations of H. fraxineus hyphae were observed: the development of apical or intercalary cytoplasmic extrusions, development of internal hyphae of the test fungi in pathogens’ hyphae, the deformation and disruption of significant sections of H. fraxineus hyphae via lysis and mycoparasitism, complete desolation of H. fraxineus cells and breakdown of hyphae into short fragments, and disappearing of pigment in the affected hyphae of H. fraxineus. The inoculation tests performed in vivo or in glass Petrie dishes showed that all the identified taxa were able to lead to pathological changes in H. fraxineus apothecia, and the mycelium of some of them completely covered pseudosclerotial plates of H. fraxineus. It was emphasized in the discussion that such activity of these fungi in forest stands may contribute to the reduction in the H. fraxineus inoculum reservoir. Full article

(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System)

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15 pages, 2263 KiB

Open AccessArticle

Agricultural Crops Grown in Laboratory Conditions on Chernevaya Taiga Soil Demonstrate Unique Composition of the Rhizosphere Microbiota

by Irina Kravchenko, Mikhail Rayko, Ekaterina Tikhonova, Aleksey Konopkin, Evgeny Abakumov and Alla Lapidus

Microorganisms 2022, 10(11), 2171; https://doi.org/10.3390/microorganisms10112171 - 31 Oct 2022

Cited by 4 | Viewed by 1728

Abstract

Chernevaya taiga in West Siberia is a unique environment, with gigantism of grasses and shrubs. Exceptionally high productivity of plants is determined by the synergistic interaction of various factors, with a special role belonging to microorganisms colonizing the plant roots. This research explored [...] Read more.

Chernevaya taiga in West Siberia is a unique environment, with gigantism of grasses and shrubs. Exceptionally high productivity of plants is determined by the synergistic interaction of various factors, with a special role belonging to microorganisms colonizing the plant roots. This research explored whether agricultural plants can recruit specific microorganisms from within virgin Chernevaya Umbrisol and thus increase their productivity. Radish and wheat plants were grown on the Umbrisol (T1) and control Retisol of Scotch pine forest stand (T3) soils in the phytotron, and then a bacterial community analysis of the rhizosphere was performed using high-throughput sequencing of the 16S rRNA genes. In laboratory experiments, the plant physiological parameters were significantly higher when growing on the Umbrisol as compared to the Retisol. Bacterial diversity in T1 soil was considerably higher than in the control sample, and the principal coordinate analysis demonstrated apparent differences in the bacterial communities associated with the plants. Agricultural plants growing in the T1 soil form specific prokaryotic communities, with dominant genera Chthoniobacter, Pseudomonas, Burkholderia, and Massilia. These communities also include less abundant but essential for plant growth nitrifiers Cand. Nitrosocosmius and Nitrospira, and representatives of Proteobacteria, Bacilli, and Actinobacteria, known to be gibberellin-producers. Full article

(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System)

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