Soil biology

@book{burges1967soil1,
    author = "Burges, A. and Raw, F",
    title = "Soil Biology",
    year = "1967",
    publisher = "New York, Academic Press, 532 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Burges, A., and Raw, F., 1967, Soil Biology: New York, Academic Press, 532 p.}"
}

@article{mccalla1969soil,
    author = "McCALLA, T. M.",
    title = "Soil Biology",
    year = "1969",
    journal = "Soil Science",
    url = "https://doi.org/10.1097/00010694-196909000-00017",
    doi = "10.1097/00010694-196909000-00017",
    number = "3",
    pages = "229",
    volume = "108"
}

@article{macfadyen1970soil,
    author = "MACFADYEN, AMYAN",
    title = "Soil Biology",
    year = "1970",
    journal = "Nature",
    url = "https://doi.org/10.1038/227532b0",
    doi = "10.1038/227532b0",
    number = "5257",
    pages = "532-532",
    volume = "227"
}

@article{dring1971soil,
    author = "Dring, D. M. and Burges, A. and Raw, F.",
    title = "Soil Biology",
    year = "1971",
    journal = "Kew Bulletin",
    url = "https://doi.org/10.2307/4103187",
    doi = "10.2307/4103187",
    number = "3",
    pages = "411",
    volume = "25"
}

@incollection{ugolini1983soil,
    author = "Ugolini, F.C. and Edmonds, R.L.",
    title = "Soil Biology",
    year = "1983",
    booktitle = "Developments in Soil Science",
    url = "https://doi.org/10.1016/s0166-2481(08)70602-0",
    doi = "10.1016/s0166-2481(08)70602-0",
    pages = "193-231"
}

@book{wood1989soil,
    author = "Wood, Martin",
    title = "Soil Biology",
    year = "1989",
    url = "https://doi.org/10.1007/978-1-4615-7868-0",
    doi = "10.1007/978-1-4615-7868-0"
}

@article{doi1023072261129,
    author = "Baillie, I. and Anderson, J. and Ingram, J.",
    title = "Tropical Soil Biology and Fertility: A Handbook of Methods.",
    year = "1990",
    journal = "Journal of Ecology",
    url = "https://www.semanticscholar.org/paper/fd08d0e4326a8686e784f011a6181b873c7b85ad",
    doi = "10.2307/2261129",
    is_oa = "true",
    number = "2",
    pages = "547",
    semanticscholar_citation_count = "3230",
    semanticscholar_id = "fd08d0e4326a8686e784f011a6181b873c7b85ad",
    volume = "78"
}

@incollection{weston2004soil,
    author = "Weston, C.J. and Whittaker, K.L.",
    title = "SOIL BIOLOGY AND TREE GROWTH | Soil Biology",
    year = "2004",
    booktitle = "Encyclopedia of Forest Sciences",
    url = "https://doi.org/10.1016/b0-12-145160-7/00248-9",
    doi = "10.1016/b0-12-145160-7/00248-9",
    pages = "1183-1189"
}

@misc{kladivko2011soil,
    author = "Kladivko, Eileen J. and Clapperton, M. Jill",
    title = "Soil Biology",
    year = "2011",
    booktitle = "ASA, CSSA, and SSSA Books",
    url = "https://doi.org/10.2136/2011.soilmanagement.c9",
    doi = "10.2136/2011.soilmanagement.c9",
    pages = "145-160"
}

@incollection{crossref2014soil,
    title = "soil biology",
    year = "2014",
    booktitle = "Dictionary Geotechnical Engineering/Wörterbuch GeoTechnik",
    url = "https://doi.org/10.1007/978-3-642-41714-6\_195059",
    doi = "10.1007/978-3-642-41714-6\_195059",
    pages = "1263-1263"
}

@book{crossref2018soil,
    title = "Soil Biology",
    year = "2018",
    url = "https://doi.org/10.1201/9781351076692",
    doi = "10.1201/9781351076692"
}

@article{doi101016jgeoderma201710041,
    author = "Choudhary, M. and Datta, A. and Jat, H. and Yadav, A. and Gathala, M. and Sapkota, T. and Das, Amitabha and Sharma, P. C. and Jat, M. L. and Singh, Rajbir and Ladha, J.",
    title = "Changes in soil biology under conservation agriculture based sustainable intensification of cereal systems in Indo-Gangetic Plains",
    year = "2018",
    journal = "Geoderma",
    url = "https://escholarship.org/content/qt6v03r1wr/qt6v03r1wr.pdf?t=rtpz0f",
    doi = "10.1016/J.GEODERMA.2017.10.041",
    is_oa = "true",
    pages = "193-204",
    semanticscholar_citation_count = "170",
    semanticscholar_id = "b7c885cccaabc9f3aa2e63cf5e2452dabca4d922",
    volume = "313"
}

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). Here we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negatively correlated with the abundance of the isolate’s closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust. Metagenomic sequencing provides a window into microbial community structure and metabolic potential. Here, Swenson et al. integrate metabolomics and shotgun sequencing to functionally link microbial community structure with environmental chemistry in biological soil crust (biocrust).

@article{doi101038s41467017023569,
    author = "Swenson, Tami L. and Karaoz, U. and Swenson, Joel M. and Bowen, B. and Northen, T.",
    title = "Linking soil biology and chemistry in biological soil crust using isolate exometabolomics",
    year = "2018",
    journal = "Nature Communications",
    abstract = "Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). Here we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70\% are negatively correlated with the abundance of the isolate’s closest matching environmental relative in situ, whereas for released metabolites, 67\% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust. Metagenomic sequencing provides a window into microbial community structure and metabolic potential. Here, Swenson et al. integrate metabolomics and shotgun sequencing to functionally link microbial community structure with environmental chemistry in biological soil crust (biocrust).",
    url = "https://www.nature.com/articles/s41467-017-02356-9.pdf",
    doi = "10.1038/s41467-017-02356-9",
    is_oa = "true",
    number = "1",
    semanticscholar_citation_count = "156",
    semanticscholar_id = "ba917d1d7593603c7f7fa276bfc63113fbc4f1f1",
    volume = "9"
}

Protists include all eukaryotes except plants, fungi and animals. They are an essential, yet often forgotten, component of the soil microbiome. Method developments have now furthered our understanding of the real taxonomic and functional diversity of soil protists. They occupy key roles in microbial foodwebs as consumers of bacteria, fungi and other small eukaryotes. As parasites of plants, animals and even of larger protists, they regulate populations and shape communities. Pathogenic forms play a major role in public health issues as human parasites, or act as agricultural pests. Predatory soil protists release nutrients enhancing plant growth. Soil protists are of key importance for our understanding of eukaryotic evolution and microbial biogeography. Soil protists are also useful in applied research as bioindicators of soil quality, as models in ecotoxicology and as potential biofertilizers and biocontrol agents. In this review, we provide an overview of the enormous morphological, taxonomical and functional diversity of soil protists, and discuss current challenges and opportunities in soil protistology. Research in soil biology would clearly benefit from incorporating more protistology alongside the study of bacteria, fungi and animals.

@article{doi101093femsrefuy006,
    author = "Geisen, Stefan and Mitchell, Edward A. D. and Adl, Sina M. and Bonkowski, Michael and Dunthorn, Micah and Ekelund, Flemming and Fernández, Leonardo D. and Jousset, Alexandre and Krashevska, Valentyna and Singer, David and Spiegel, Frederick W. and Walochnik, Julia and Lara, Enrique",
    title = "Soil protists: a fertile frontier in soil biology research",
    year = "2018",
    journal = "FEMS Microbiology Reviews",
    abstract = "Protists include all eukaryotes except plants, fungi and animals. They are an essential, yet often forgotten, component of the soil microbiome. Method developments have now furthered our understanding of the real taxonomic and functional diversity of soil protists. They occupy key roles in microbial foodwebs as consumers of bacteria, fungi and other small eukaryotes. As parasites of plants, animals and even of larger protists, they regulate populations and shape communities. Pathogenic forms play a major role in public health issues as human parasites, or act as agricultural pests. Predatory soil protists release nutrients enhancing plant growth. Soil protists are of key importance for our understanding of eukaryotic evolution and microbial biogeography. Soil protists are also useful in applied research as bioindicators of soil quality, as models in ecotoxicology and as potential biofertilizers and biocontrol agents. In this review, we provide an overview of the enormous morphological, taxonomical and functional diversity of soil protists, and discuss current challenges and opportunities in soil protistology. Research in soil biology would clearly benefit from incorporating more protistology alongside the study of bacteria, fungi and animals.",
    url = "https://doi.org/10.1093/femsre/fuy006",
    doi = "10.1093/femsre/fuy006",
    openalex = "W2791265185",
    references = "doi101111j14610248201101634x"
}

1. Soil organisms 1.1. Bacteria 1.2. Actinomycetes 1.3. Fungi 1.4. Algae 1.5. Mycorrhizae 1.6. Lichens 1.7. Microfauna 1.8. Mesofauna 1.9. Macrofauna 2. Soil biological processes 2.1. Decomposition 2.2. Mineralization-immobilization 2.3. Nitrification 2.4. Denitrification 2.5. Biological nitrogen fixation 2.6. Rhizosphere processes 2.7. Soil structure formation 3. State of the art in soil biology 3.1. Soil microbial diversity 3.2. Enzymes 3.3. Soil organic matter characterization 3.4. Quantification of soil microbial biomass 3.5. Bioremediation 3.6. Decomposition 3.7. Soil quality 3.8. Soil carbon sequestration 4. Concluding remarks Glossary Bibliography Biographical Sketch

@article{doi1010179781316809785012,
    author = "Franzluebbers, A.",
    title = "Soil Biology",
    year = "2019",
    journal = "Properties and Management of Soils in the Tropics",
    booktitle = "Properties and Management of Soils in the Tropics",
    abstract = "1. Soil organisms 1.1. Bacteria 1.2. Actinomycetes 1.3. Fungi 1.4. Algae 1.5. Mycorrhizae 1.6. Lichens 1.7. Microfauna 1.8. Mesofauna 1.9. Macrofauna 2. Soil biological processes 2.1. Decomposition 2.2. Mineralization-immobilization 2.3. Nitrification 2.4. Denitrification 2.5. Biological nitrogen fixation 2.6. Rhizosphere processes 2.7. Soil structure formation 3. State of the art in soil biology 3.1. Soil microbial diversity 3.2. Enzymes 3.3. Soil organic matter characterization 3.4. Quantification of soil microbial biomass 3.5. Bioremediation 3.6. Decomposition 3.7. Soil quality 3.8. Soil carbon sequestration 4. Concluding remarks Glossary Bibliography Biographical Sketch",
    url = "https://www.semanticscholar.org/paper/2dd85267769f1474c548cfa22cd96e6fbae69f40",
    doi = "10.1017/9781316809785.012",
    is_oa = "true",
    pages = "236-258",
    semanticscholar_citation_count = "167",
    semanticscholar_id = "2dd85267769f1474c548cfa22cd96e6fbae69f40"
}

High soil temperature due to climate change may influence nutrient mineralization and soil biology. An incubation study was conducted at Bangladesh Rice Research Institute to determine the effect of temperature (28°C and 45°C) on nutrient mineralization and soil microbial population of two different soils (terrace and saline soil) having different nutrient management practices (chemical fertilizer and integrated nutrient management). Terrace soil was clay loam and saline (6 ds m-1) soil was sandy loam in texture. Total N and organic C content was significantly high in terrace soil compared to saline soil. High temperature (45°C) enhanced C mineralization by 33% in integrated nutrient management (INM) of terrace soil and 41% in chemical fertilizer treatment in saline soil. The NH4+-N mineralization was increased by 3 fold in saline soil at 45°C as compared to the same at normal temperature of 28°C. Temperature and nutrient management options also significantly influenced phosphorus (P) and potassium (K) mineralization. High temperature significantly enhanced P mineralization in INM compared to chemical fertilizer amendment. In terrace soil, at 28°C temperature K mineralization was high in chemical fertilizer amended soil as compared to INM treatment. Temperature and nutrient sources affected soil bacterial population significantly compared to fungi, and actinomycetes. Phosphate solubilizing bacteria (PSB) were more resistant to high temperature compared to free-living N2 fixing bacteria. In general, high temperature and nutrient management practices affected C, N, P, K mineralization and soil biology; although mode of action varied and depending on soil types and nutrient management practices.

@article{doi1017576jsm2019480405,
    author = "Naher, U. A. and Sarker, I. and Jahan, A. and Maniruzzaman, M. and Choudhury, A. and Kalra, N. and Biswas, J.",
    title = "Nutrient Mineralization and Soil Biology as Influenced by Temperature and Fertilizer Management Practices",
    year = "2019",
    journal = "Sains Malaysiana",
    abstract = "High soil temperature due to climate change may influence nutrient mineralization and soil biology. An incubation study was conducted at Bangladesh Rice Research Institute to determine the effect of temperature (28°C and 45°C) on nutrient mineralization and soil microbial population of two different soils (terrace and saline soil) having different nutrient management practices (chemical fertilizer and integrated nutrient management). Terrace soil was clay loam and saline (6 ds m-1) soil was sandy loam in texture. Total N and organic C content was significantly high in terrace soil compared to saline soil. High temperature (45°C) enhanced C mineralization by 33\% in integrated nutrient management (INM) of terrace soil and 41\% in chemical fertilizer treatment in saline soil. The NH4+-N mineralization was increased by 3 fold in saline soil at 45°C as compared to the same at normal temperature of 28°C. Temperature and nutrient management options also significantly influenced phosphorus (P) and potassium (K) mineralization. High temperature significantly enhanced P mineralization in INM compared to chemical fertilizer amendment. In terrace soil, at 28°C temperature K mineralization was high in chemical fertilizer amended soil as compared to INM treatment. Temperature and nutrient sources affected soil bacterial population significantly compared to fungi, and actinomycetes. Phosphate solubilizing bacteria (PSB) were more resistant to high temperature compared to free-living N2 fixing bacteria. In general, high temperature and nutrient management practices affected C, N, P, K mineralization and soil biology; although mode of action varied and depending on soil types and nutrient management practices.",
    url = "https://doi.org/10.17576/jsm-2019-4804-05",
    doi = "10.17576/JSM-2019-4804-05",
    is_oa = "true",
    number = "4",
    pages = "735-744",
    semanticscholar_citation_count = "12",
    semanticscholar_id = "7f7a1b35ba4d1d84c31d935e43a4e389d3e4140e",
    volume = "48"
}

@article{doi101007s00374021015482,
    author = "Cai, Y. J. and Ok, Y. and Lehmann, J. and Chang, S. X.",
    title = "Recommendations for stronger biochar research in soil biology and fertility",
    year = "2021",
    journal = "Biology and Fertility of Soils",
    url = "https://link.springer.com/content/pdf/10.1007/s00374-021-01548-2.pdf",
    doi = "10.1007/s00374-021-01548-2",
    is_oa = "true",
    number = "3",
    pages = "333-336",
    semanticscholar_citation_count = "22",
    semanticscholar_id = "59df894d98266fddbfecc4a340a2e9113df148fe",
    volume = "57"
}

@article{doi101016jscitotenv2021148787,
    author = "Blaise, D. and Velmourougane, K. and Santosh, S. and Manikandan, A.",
    title = "Intercrop mulch affects soil biology and microbial diversity in rainfed transgenic Bt cotton hybrids.",
    year = "2021",
    journal = "The Science of the total environment",
    url = "https://www.semanticscholar.org/paper/7d812620565febd64038403cf8c156483f57aba9",
    doi = "10.1016/j.scitotenv.2021.148787",
    is_oa = "true",
    pages = "148787",
    semanticscholar_citation_count = "23",
    semanticscholar_id = "7d812620565febd64038403cf8c156483f57aba9",
    volume = "794"
}

Since management practices profoundly influence soil characteristics, the adoption of sustainable agro-ecological practices is essential for soil health conservation. We compared soil health in organic and conventional fields in the Abruzzi region (central Italy) by using (1) the soil biology quality (QBS) index (which expresses the level of specialisation in soil environment shown by microarthropods) and (2) microarthropod diversity expressed by Hill numbers. QBS values were calculated using both the original formulation based on only presence/absence data and a new abundance-based version. We found that organic management improves soil biology quality, which encourages the use of organic farming to maintain soil health. Including arthropod abundance in QBS calculation does not change the main outcomes, which supports the use of its original, speedier formulation. We also found that agricultural fields included in protected areas had greater soil health, which shows the importance of the matrix in determining agricultural soil health and highlights the importance of land protection in preserving biodiversity even in managed soils. Finally, we found that soil biology quality and microarthropod community structure are distinctly influenced by certain physical and chemical characteristics of the soil, which supports the use of microarthropods as biological indicators.

@article{doi103390agriculture11101022,
    author = "Mantoni, Cristina and Pellegrini, M. and Dapporto, L. and del Gallo, Maddalena and Pace, L. and Silveri, D. and Fattorini, S.",
    title = "Comparison of Soil Biology Quality in Organically and Conventionally Managed Agro-Ecosystems Using Microarthropods",
    year = "2021",
    journal = "Agriculture",
    abstract = "Since management practices profoundly influence soil characteristics, the adoption of sustainable agro-ecological practices is essential for soil health conservation. We compared soil health in organic and conventional fields in the Abruzzi region (central Italy) by using (1) the soil biology quality (QBS) index (which expresses the level of specialisation in soil environment shown by microarthropods) and (2) microarthropod diversity expressed by Hill numbers. QBS values were calculated using both the original formulation based on only presence/absence data and a new abundance-based version. We found that organic management improves soil biology quality, which encourages the use of organic farming to maintain soil health. Including arthropod abundance in QBS calculation does not change the main outcomes, which supports the use of its original, speedier formulation. We also found that agricultural fields included in protected areas had greater soil health, which shows the importance of the matrix in determining agricultural soil health and highlights the importance of land protection in preserving biodiversity even in managed soils. Finally, we found that soil biology quality and microarthropod community structure are distinctly influenced by certain physical and chemical characteristics of the soil, which supports the use of microarthropods as biological indicators.",
    url = "https://www.mdpi.com/2077-0472/11/10/1022/pdf?version=1635663305",
    doi = "10.3390/agriculture11101022",
    is_oa = "true",
    number = "10",
    pages = "1022",
    semanticscholar_citation_count = "27",
    semanticscholar_id = "776164d9d2868933e66fe9cf3615fb878c38bcf2",
    volume = "11"
}

Arbuscular mycorrhizal (AM) fungi (e.g., Rhizophagus species) recruit specific bacterial species in their hyphosphere. However, the chemical interplay and the mutual benefit of this intricate partnership have not been investigated yet, especially as it involves bacteria known as strong producers of antifungal compounds such as Bacillus velezensis. Here, we show that the soil-dwelling B. velezensis migrates along the hyphal network of the AM fungus R. irregularis, forming biofilms and inducing cytoplasmic flow in the AM fungus that contributes to host plant root colonization by the bacterium. During hyphosphere colonization, R. irregularis modulates the biosynthesis of specialized metabolites in B. velezensis to ensure stable coexistence and as a mechanism to ward off mycoparasitic fungi and bacteria. These mutual benefits are extended into a tripartite context via the provision of enhanced protection to the host plant through the induction of systemic resistance.

@article{doi101016jcub202409019,
    author = "Anckaert, Adrien and Declerck, Stéphane and Poussart, Laure-Anne and Lambert, Stéphanie and Helmus, Catherine and Boubsi, Farah and Steels, Sébastien and Argüelles-Arias, Anthony and Calonne-Salmon, Maryline and Ongena, M.",
    title = "The biology and chemistry of a mutualism between a soil bacterium and a mycorrhizal fungus.",
    year = "2024",
    journal = "Current biology : CB",
    abstract = "Arbuscular mycorrhizal (AM) fungi (e.g., Rhizophagus species) recruit specific bacterial species in their hyphosphere. However, the chemical interplay and the mutual benefit of this intricate partnership have not been investigated yet, especially as it involves bacteria known as strong producers of antifungal compounds such as Bacillus velezensis. Here, we show that the soil-dwelling B. velezensis migrates along the hyphal network of the AM fungus R. irregularis, forming biofilms and inducing cytoplasmic flow in the AM fungus that contributes to host plant root colonization by the bacterium. During hyphosphere colonization, R. irregularis modulates the biosynthesis of specialized metabolites in B. velezensis to ensure stable coexistence and as a mechanism to ward off mycoparasitic fungi and bacteria. These mutual benefits are extended into a tripartite context via the provision of enhanced protection to the host plant through the induction of systemic resistance.",
    url = "https://www.semanticscholar.org/paper/ac09db6fce73bf978316dc647662b91bf195312d",
    doi = "10.1016/j.cub.2024.09.019",
    is_oa = "true",
    number = "21",
    pages = "4934-4950.e8",
    semanticscholar_citation_count = "39",
    semanticscholar_id = "ac09db6fce73bf978316dc647662b91bf195312d",
    volume = "34"
}

@misc{crossrefNonesoil,
    title = "Soil Biology",
    year = "None",
    booktitle = "SpringerReference",
    url = "https://doi.org/10.1007/springerreference\_77150",
    doi = "10.1007/springerreference\_77150"
}