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Agricultural Land Use Influences Bacteriophage Community Diversity, Richness, and Heterogeneity

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Abstract

The last two decades have witnessed a large-scale conversion of crop cultivation areas into small and mid-sized tea plantations in Assam, India. Agricultural land-use pattern positively or negatively influences native hydrology and above- and belowground biodiversity. Very little is known about the effect of agricultural land-use patterns on the soil virus (especially, bacteriophage) community structure and function. This metagenomic-based study evaluated the rhizosphere viral community structure of three interlinked cultivation areas, viz., mixed cropping area (coded as CP1), tea-seed orchard (CP2), and monocropping tea cultivation (CP3). The bacteriophages belonged to four major classes with the dominance of Malgrandaviricetes (CP1: 79.37%; CP2: 64.62%; CP3: 4.85%) followed by Caudoviricetes (CP1: 20.49%; CP2: 35.22%; CP3: 90.29%), Faserviricetes (CP1: 0.03%; CP2: 0.08%; CP3: 3.88%), and Tectiliviricetes (CP1: 0.12%; CP2: 0.07%; CP3: 0.97%). Microviruses dominated the phage population in both CP1 and CP2, representing 79.35% and 64.59% of total bacteriophage abundance. Both CP1 and CP2 had higher bacteriophage richness (species richness, R in CP1: 65; R in CP2: 66) and lower evenness (Pielou's evenness index, J in CP1: 0.531; J in CP2: 0.579) compared to the CP3 (R: 30; J: 0.902). Principal component analysis of edaphic soil factors and bacteriophage community structure showed a reverse-proportional correlation between the levels of Al saturation, and exchangeable Al3+ ions with that of soil pH, and bacteriophage abundance. Our study indicates that monocropping tea cultivation soil bears less viral richness, abundance, and heterogeneity.

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Data Availability

The metagenomic sequence reads are available on the NCBI database with accession numbers PRJNA797555 (for the CP1 sample) and PRJNA698063 (for samples, CP2 and CP3). The MG-RAST Ids for the metagenomes are as follows: CP1: mgm4926379.3; CP2: mgm4916718.3; CP3: mgm4528392.3.

Code Availability

Not applicable.

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Authors and Affiliations

  1. DBT-North East Centre for Agricultural Biotechnology (DBT-NECAB), Assam Agricultural University, Jorhat, Assam, India

    Sudipta Sankar Bora, Abhisek Dasgupta & Madhumita Barooah

  2. Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India

    Romen Singh Naorem, Dibya Jyoti Hazarika, Amrita Churaman & Madhumita Barooah

  3. Department of Tea Husbandry and Technology, Assam Agricultural University, Jorhat, Assam, India

    Manuranjan Gogoi

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  1. Sudipta Sankar Bora
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Contributions

MB and SSB contributed to conceptualization. SSB, RSN, and AC contributed to methodology. DJH, NRS, AD, and AC contributed to formal analysis and investigation. SSB contributed to writing—original draft preparation. MB and DJH contributed to writing—review and editing. MB contributed to funding acquisition and supervision. MG and MB contributed to resources.

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Correspondence to Madhumita Barooah.

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Bora, S.S., Naorem, R.S., Hazarika, D.J. et al. Agricultural Land Use Influences Bacteriophage Community Diversity, Richness, and Heterogeneity. Curr Microbiol 80, 10 (2023). https://doi.org/10.1007/s00284-022-03129-4

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