Soil bacterial and fungal community structure of a rice monoculture and rice-pasture rotation systems

Maguire, Vanina G; Bordenave, César Daniel; Nieva, Amira Susana del Valle; Llames, María Eugenia del Rosario; Colavolpe, Belén; Gárriz, Andrés; Ruíz, Oscar Adolfo

doi:10.1016/j.apsoil.2020.103535

Cited by 45 publications

(28 citation statements)

References 86 publications

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“…Our findings indicate that bacterial communities are more diverse than fungal communities. Similar results have been reported in rice-rotation systems ( Ma et al, 2020 ; Maguire et al, 2020 ) and other rice co-culture systems ( Li et al, 2018 ; Hou et al, 2021 ). Compared to fungi, bacteria may be more abundant in these systems because their range of metabolic and nutritional strategies enables them to adapt to more complex ecological niches and habitats.…”

Section: Discussionsupporting

confidence: 89%

Impact of Dietary Protein Content on Soil Bacterial and Fungal Communities in a Rice–Crab Co-culture System

et al. 2021

Front. Microbiol.

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Although co-culture of paddy fields with aquatic animals is lucrative, the ecological impacts of high-protein content entering the agricultural soil via animal pellet feed and feces have not been well studied. Moreover, the effects of dietary protein on soils and soil microbes remain unclear. To elucidate this, we examined soil bacterial and fungal community composition and temporal changes in paddy fields subjected to different protein-content diets via 16S/18S rRNA gene amplicon sequencing analysis with a high-throughput next-generation sequencer. MiSeq sequencing revealed that protein content significantly impacted fungal community structure. High-protein diets reduced bacterial community diversity and relative abundance in both July and October. The phylum-level bacterial taxonomic composition was not affected by diet treatment, while in fungi, a major phylum-level shift was evident. Hierarchically clustered analysis showed that high-protein diets significantly reduced the relative abundance of Brevundimonas in both July and October. Saprotrophic macrofungal diversity was negatively related to dietary protein content. Considering microbial community structure and environmental factors, ca. 15% protein content is appropriate for the rice-crab co-culture system that we studied.

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Section: Discussionsupporting

confidence: 89%

Impact of Dietary Protein Content on Soil Bacterial and Fungal Communities in a Rice–Crab Co-culture System

et al. 2021

Front. Microbiol.

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“…Similarly, Acidobacteria is known to degrade plant residue multimers [79] . Proteobacteria, Actinobacteria, Acidobacteria, and Curvularia were found to be the main bacterial phyla in rice plant soils after the different treatments, in agreement with the results reported by Maguire et al [29] . In contrast, Xu et al [80] found that the top four most abundant phyla were Proteobacteria, Chloroflexi, Bacteriodetes, and Firmicutes.…”

Section: Bacteria Affect Soil Nutrient Supplysupporting

confidence: 92%

“…The simultaneous inoculation of endophytic and rhizospheric bacteria has been found to increase soil nitrogen [27] . Many bacteria and fungi are found in soil, and as the structure of the bacterial community changes, the fungal community also changes [28,29] . Thus, inoculating a plant growth promoting bacteria (PGPB) and a plant growth promoting fungus (PGPF) into the soil at the same time increases the capacity for improving the soil environment.…”

Section: Introduction 1mentioning

confidence: 99%

Effects of Bacillus subtilis and Saccharomyces cerevisiae inoculation on soil bacterial community and rice yield under combined irrigation with reclaimed and fresh water

Lu,

Qi,

et al. 2022

International Journal of Agricultural and Biological Engineering

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In order to save fresh water and reduce soil salt accumulation, reclaimed water-fresh water combined irrigation, i.e, irrigation with reclaimed water for 50 d and then with fresh water till harvest, was used in rice planting. Bacillus subtilis and Saccharomyces cerevisiae were inoculated into the soil at the end of reclaimed water irrigation. The inoculation weight per pot of these microorganisms was as follows: 0 g and 0 g (J0), 5 g and 0 g (J1), 3.75 g and 1.25 g (J2), 2.5 g and 2.5 g (J3), 1.25 g and 3.75 g (J4), and 0 g and 5 g (J5), respectively. Treatment using reclaimed water in the whole stage was used as the control (CK). The plant height, tiller, physical and chemical properties of the soil, and soil bacterial diversity were measured. It was found that the plant height of rice was increased significantly by J1-J5 treatments. The dry weight of rice root, stem, and panicle and the 1000-grain weight increased significantly, while the leaf dry weight decreased. Microorganism inoculation significantly increased the nutrient absorption capacity of the crops. J1, J2, and J4 treatments significantly increased the amount of nitrate-nitrogen, ammonium nitrogen, available phosphorus, and available potassium, while J3, J4, and J5 treatments increased the soil organic matter, and microbial inoculation significantly decreased the EC of soil. J4 treatment induced the largest reduction in EC, and microorganisms treatments increased soil pH. Bacterial function prediction based on the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway indicated that soil metabolic function was not significantly disturbed by the treatments. Organic matter and pH are the two main factors affecting the structure of the bacterial community in soil. 3.75 g of B. subtilis and 1.25 g of S. cerevisiae per pot is the best inoculation ratio.

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“…However, little is known about how different rice rotations affect soil microbial communities and how it affects the productivity and sustainability of these systems in temperate regions like Uruguay. Previous studies showed no major differences among microbial communities associated with regards to rice and pasture rotations and soils under continuous rice in South America (Fernández et al, 2013;Maguire et al, 2020).…”

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confidence: 91%

Microbial community structure in rice, crops, and pastures rotation systems with different intensification levels in the temperate region of Uruguay

Martínez

2021

Preprint

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Rice is an important crop in Uruguay associated mostly with livestock production in a rice and pasture rotation system since the 1920s. However, in recent years there has been interest in intensifying the production in some of these systems to satisfy market demands and increase income. Intensification occurs by augmenting the rice frequency in the rotation, including new crops like sorghum and soybean, or shortening the pasture phase. A long-term experiment was established in 2012 in the main rice producing area of Uruguay with the objective to study the impact of intensification in rice rotations. After the first cycle of rotation soils from seven rotation phases were sampled and microbial communities were studied by means of high-throughput sequencing of Illumina NovaSeq 6000. Archaeal/bacterial and fungal community composition were studied (16S rRNA and 18S gene regions) detecting 3662 and 807 bacterial and fungal Operational Taxonomic Units (OTUs), respectively. Actinobacteria, Firmicutes and Proteobacteria were the most common bacterial phyla. Among them, only Proteobacteria differed significantly between rotations. Although most fungal OTUs were unidentified, Ascomycota, Basidiomycota and Mucoromycota were the most abundant fungal classes within identified taxa. Bacterial communities differed between rotations forming three groups according to the percentage of rice in the system. Fungal communities clustered in four groups, although not well differentiated, and mostly associated with the antecessor crop. Only P and C:N varied between rotations among soil physicochemical variables after six years, and individual bacterial OTUs appeared weakly influenced by P, pH, Mg and fungal OTUs by P. The results suggest that after six years, bacteria/archaeal communities were influenced by the time with rice in the rotation, and fungal communities were more influenced by the antecessor crop. More studies are needed to associate fungal communities with certain rotational or environmental variables. Some taxa were associated with a particular rotation, and some bacterial taxa were identified as biomarkers. Fungal indicator taxa were not identified at the species level for any rotation.

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Soil bacterial and fungal community structure of a rice monoculture and rice-pasture rotation systems

Cited by 45 publications

References 86 publications

Impact of Dietary Protein Content on Soil Bacterial and Fungal Communities in a Rice–Crab Co-culture System

Impact of Dietary Protein Content on Soil Bacterial and Fungal Communities in a Rice–Crab Co-culture System

Effects of Bacillus subtilis and Saccharomyces cerevisiae inoculation on soil bacterial community and rice yield under combined irrigation with reclaimed and fresh water

Microbial community structure in rice, crops, and pastures rotation systems with different intensification levels in the temperate region of Uruguay

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