soil biology experts

soil biology experts

Advancements in Soil Biology Research: From Microbial Interactions to Ecosystem Dynamics

1. Introduction to Soil Biology

Soil biological processes underpin the provisioning of ecosystem goods and services in terrestrial ecosystems. Examples of terrestrial ecosystem services include the provision of food and fiber production, decomposition of organic matter, formation of the soil structure, and protection of water resources. Soil biological processes are also largely responsible for mineral nutrient cycling, for the maintenance of a diverse assemblage of species including many of the world’s livestock and crops, and for the regulation of greenhouse gases. In addition, soil biological processes also support many cultural ecosystem services such as recreational activities and aesthetic values associated with the terrestrial environment. Despite the critical roles that soils play in terms of regulating the Earth’s climate, atmospheric gases, and precipitation, as well as valuing several other ecosystem services, scientific understanding of soil biological processes is only now emerging as a central theme in molecular ecology and ecotechnology.

Soil biological processes are indeed complex, as they routinely involve interactions among many different organisms (e.g. plants, animals, fungi, bacteria, etc.) and multiple biotic and abiotic components of the above- and below-ground environment. Essentially, soil biology includes the study of the roles of various and diverse life-forms as well as their dynamic interactions with one another in relation to soil chemical and physical processes. Key role players in soil biology include a myriad of microbial and faunal groups interacting with plant roots and associated symbiotic mycorrhizal fungi, as both living and freshly attributable residues. Conceptual models of these ecological dynamisms are being investigated at a range of ecological and soil mycological subdisciplines and in a variety of soil and environmental management contexts. Based on these models, there is great potential for applications that integrate soil microbiology and plant breeding in order to promote better uses of traditionally underutilized crops by commercial agriculture while also offering promising ways to ease or manage the atmospheric CO2 levels.

2. Microbial Communities in Soil

Soil microorganisms are referred to as soil flora, which conceal a wide range of diversity. Also, soil microorganisms are highly exposed to environmental fluctuations due to soil heterogeneity on various scales. The soil microbiome is the totality of soil microorganisms capable of living in soil, including their genomic and protein reserves, and the interactions between these microorganisms and the physical and chemical properties of the soil. Soil microbes play a crucial role in maintaining ecosystem sustainability. Approximately 10% of soil contains dissolved organic carbon mainly produced by root exudates, root respiration, litter decomposition, and manure application. When compared to the amount of plant sap flow, plant microbial communities potentially receive high levels of substrates. These substrates mainly consist of glucose, sucrose, fructose, organic acids, and polysaccharides. The glomalin-related soil protein (GRSP) and polysaccharides are the main storage proteins in the arbuscular mycorrhizal (AM) fungi, and the extracellular polysaccharide synthesized by soil bacterial cells cannot be removed by water extraction or leaching. These coatings can significantly adhere to soil structure formation, maintain soil moisture, and increase the plant available water in soil.

In general, organic matter input increases the soil microbial biomass and activity. Soil microorganisms are responsible for soil organic matter mineralization processes involving carbon and other nutrient cycling. Plant litter, root detritus, and manure are the basic resources for organic carbon additions to the soil. Primarily, soil carbon-limited substrates are classified as cellulose derived from plant cell walls, lignin that terpenoids polymerize with cellulose polymers, and soil organic matter. During the growing period, more substrates are carbohydrates, proteins, lipids, and byproducts. When considering soil carbon, the optimal rhizodeposition metabolic strategy is synthesizing phytochemicals or antibiotic-stress compounds. The phytochemicals (salicylates, flavonoids, and tannins) act as attractants or repellents for mycorrhizal fungi and root-associated beneficial bacteria. These mutualistic microorganisms attract more hyphae and promote root hair elongation during primary root growth. Additionally, other fungal mycelium and rhizospheric bacteria produce signaling molecules that interact with plant roots.

3. Soil Fauna and their Ecological Roles

Soil fauna are essential not only for soil fertility, but also for food production, atmosphere, and biogeochemistry. Soil fauna have their own ecological niches that they occupy. Bacteria and fungi, for example, play an essential role in nutrient cycling by breaking down complex organic molecules and are the preferred food source for numerous protists and many nematodes. Microarthropods function as herbivores, influencing fungal and bacterial biomass. Some of them are omnivorous, introducing predation into the system and form arbuscular mycorrhizal associations by feeding on arbuscules of mycorrhizal fungi. Nematodes are also devastating predators that act as a major top-down control factor for microbial communities. Larger soil fauna such as earthworms are able to change the habitat structure, transport mycorrhizal spores and mycorrhizal hyphae, and contribute significantly to litter decomposition. In complex soil communities, faunal interactions range from the interacting individuals themselves to the interactions of lower-level organisms with the ecosystem itself. These dynamics can be as complex as those in ocean or land environments.

4. The Impact of Soil Biology on Agriculture

Agriculture is both a major consumer of microbial products and the primary economic support for soil biological research. Plants have long been used as model systems, and many of the first morphological and physiological experiments were carried out on agriculturally important crops. As a result, soil biologists have access to a wealth of management and genetic resources. Real and potential applications include managing microbial communities for crop health, improving the ability of soils to sequester carbon, ramp entire food webs, and in turn becoming important in maintaining the health and diversity of soil-ecosystem services. Such considerations have led to multidisciplinary research efforts and technologies for measuring soil biology in situ. Soil communities make an important contribution to human health and quality of life, with soil animals being essential members of the farm fauna.

At a time when economies of scale increasingly dictate agricultural practices, soils underpin contentious issues of food safety and security, as well as the testing and subsequent acceptance or rejection of genetic, fertilizer, pesticide, and cultivation practices. Only by unraveling the complex interactions between soil animals and microorganisms in diverse ecosystems will we come to understand and manage these vitally important natural resources in our own best interests. Agricultural practice is influenced by soil biology in many ways. A healthy soil community can usually continue to enhance nutrient availability, maintain good structure, and detoxify pollutants as fast as they are produced. A diverse ecosystem will benefit from compensatory effects, effective top-down regulation, and fast dynamic responses, especially to disturbances such as compaction and inputs of pollutants. Heat production is a form of biological activation, resulting from the exothermic reactions of metabolic, feeding, absorption, and excretion activities. Soil gas release, which can seriously damage agricultural operations such as cotton harvesting and potato cultivation, but cause the most damage after years of boring activity by the larvae.

5. Future Directions in Soil Biology Research

Future studies should seek to test such explicitly microbial hypotheses in order to investigate: (1) the ability of microorganisms to regulate their own abundance through inhibition of microbe or enzyme production by closely related taxa, (2) genetic or enzymatic strategies for niche differentiation by closely related taxa, and (3) if different genetic or enzymatic functions known to be phylogenetically traded off against each other are encoded by related or unrelated microorganisms. For example, future experiments should investigate: (1) the ability of microorganisms to regulate their own abundance through inhibition of microbe or enzyme production by closely related taxa; (2) decrypting genetically encoded versus enzymatic strategies for niche differentiation by closely related taxa; and (3) investigating different genetic or enzymatic functions because of their trade-offs.

Future approaches to study soil biology in the field should also make full use of recent advances in molecular biology, spectroscopy, and bioinformatics. In particular, methods aimed at advancing mechanistic understanding of the diversity-based soil processes should be encouraged and could include: (1) for microorganisms, unraveling the identity of functional genes and transcribed genes and their post-translational products, metabolic profiles, and stable isotopic composition, either by employing culture-independent methods for microbes but also complementing these by culture characterizations to study the cellular activity of individual microbes or fungal genotypes with different functional potential over time and space at individual field sites; (2) for higher trophic levels, combining molecular analytical methods with life table responses, manipulative experiments, and food-web theory sound life-history-stage tailored stable isotope probing of microbe consumers, microbial prey uptake competition experiments; and (3) for ecosystem-level analysis, conducting full isotope-metagenome-transcriptome-proteome analyses and combining isotopic and biotic network research for an integrated analysis of competition and mutualism coupling plants, microbes, meso- and macro-fauna, and ecosystem processes up to litter decomposition.