Soil protists: An untapped microbial resource of agriculture and environmental importance

Protists are essential components of soil biodiversity and ecosystem functioning. They play a vital role in the microbial food web as consumers of bacteria, fungi, and other small eukaryotes and are also involved in maintaining soil fertility and plant productivity. Protists also contribute to regulating and shaping the bacterial community in terrestrial ecosystems via specific prey spectra. They play a role in plant growth promotion and plant health improvement,mostly via nutrient cycling, grazing, and the activation of bacterial genes required for plant growth and phytopathogen suppression. Thus, protists may prove to be a useful inoculant as biofertilizer and biocontrol agent. They can also be applied as model organisms as bioindicators of soil health. Despite their usefulness and essentiality, they are often forgotten and under-researched components of the soil microbiome, as most of our research focuses on bacteria and fungi. In this review, we provide an overview of the role of protists in plant productivity and plant health management and in shifts in soil bacterial community composition, as well as their roles as bioindicator. We also discuss the perspectives of knowledge gaps and future prospects to further improve soil biology.More research in soil protistology will provide insights into sustainable agriculture and environmental health alongside the study of bacteria and fungi.     

Microalgal bioinoculants for sustainable agriculture and their interactions with soil biotic and abiotic components: A review

Modern agricultural practices have posed a detrimental impact on the environment due to their intensive use to meet the food demands of an ever-increasing population. In this context, microalgal bioinoculants, specifically cyanobacteria and green microalgae, have emerged as sustainable options for agricultural practices to improve soil organic carbon, nutrient availability, microbial quality, and plant productivity. An overview of current and future perspectives on the use of microalgal bioinoculants in agriculture practices is presented in this review, along with a discussion of their interactions with soil biotic and abiotic factors that affect soil fertility, plant health, and crop productivity. The benefits of microalgal bioinoculants include releasing agronomically important metabolites (exopolymers and phytohormones) as well as solubilizing soil nutrients. Furthermore, they function as biocontrol agents against soil-borne pathogens and facilitate the establishment of rhizosphere communities of agricultural importance. So far, very few studies have explored the basic mechanisms by which microalgal bioinoculants interact with soil biotic and abiotic factors. In recent years, advanced molecular techniques have contributed to a better understanding of these interactions.     

Bacterial inoculants for rice: effects on nutrient uptake and growth promotion

Beneficial soil bacteria are able to colonize plant root systems promoting plant growth and increasing crop yield and nutrient uptake through a variety of mechanisms. These bacteria can be an alternative to chemical fertilizers without productivity loss. The objectives of this study were to test bacterial inoculants for their ability to promote nutrient uptake and/or plant growth of rice plants subjected to different rates of chemical fertilizer, and to determine whether inoculants could be an alternative to nitrogen fertilizers. To test the interaction between putatively beneficial bacteria and rice plants, field experiments were conducted with two isolates: AC32 (Herbaspirillum sp.) and UR51 (Rhizobium sp.), and different nitrogen fertilization conditions (0%, 50%, and 100% of urea). Satisfactory results were obtained in relation to the nutrient uptake by plants inoculated with both isolates, principally when the recommended amount of nitrogen fertilizer was 50% reduced. These bacterial strains were unable to increase plant growth and grain yield when plants were subjected to the high level of fertilization. This study indicated that the tested inoculant formulations can provide essential nutrients to plants, especially when the levels of nitrogen fertilizers are reduced.     

Screening of Multi-Trait Rhizobacteria for Improving the Growth,Enzyme Activities,and Nutrient Uptake of Tea (Camellia sinensis)

The use of plant growth-promoting rhizobacteria (PGPR) as agricultural inputs for increasing crop production needs the selection of efficient bacteria with plant growth-promoting (PGP) attributes. Therefore, the purpose of this study was to evaluate the effects of 20 multi-traits bacteria on tea growth, nutrient uptake, chlorophyll contents, and enzyme activities under field conditions for over 3 years. These isolates were screened in vitro for their PGP traits such as the production of indole acetic acid (IAA), nitrogenase activity, phosphorus (P) solubilization, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. Screening of rhizobacteria that show multiple PGP traits suggests that they stimulated overall plant growth, including shoot development and leaf yield, improving macro- and micro-nutrient uptake, chlorophyll contents, and activities of enzymes of tea plant. Use of strains with multiple PGP traits could be a more effective approach and have great potential for the environmentally-friendly tea production.     

Soil quality and fertility in sustainable agriculture,with a contribution to the biological classification of agricultural soils

Soils and crops are particularly vulnerable to climate change and environmental stresses. In many agrosystems, soil biodiversity and ecosystem services provided by soils are under threat from a range of natural and human drivers. Agricultural soils are often subject to agronomic practices that disrupt soil trophic networks and make soils less productive in the long term. In this scenario, sustainable soil use aimed at improving plant/root status, growth and development plays a crucial role for enhancing the biological capacity of agricultural soils. This commentary paper is divided into the following four main sections: (i) the contentious nature of soil organic matter; (ii) soil biological quality/fertility; (iii) soil classification; and, (iv) which agricultural practices can be defined as sustainable? The published literature was analyzed within a holistic framework, with agrosystems considered as living systems where soil, vegetation, fauna and microorganisms co-evolve and are reciprocally influenced. Ultimately, this article will suggest a better stewardship of agricultural soils as a natural capital.     

Soil Microbiomes—a Promising Strategy for Contaminated Soil Remediation: A Review

Bioremediation is a process mediated by microorganisms and represents a sustainable and eco-friendly way to degrade and detoxify environmental contaminants. Soil microbiomes clearly become a key component of bioremediation as they are more stable and efficient than pure cultures, being recognized as one of the scientific frontiers of the soil environmental science and technology fields. Recently, many advancements have been made regarding the investigation of remediation mechanisms by soil microbiomes and the interactions inside them. This has greatly expanded our ability to characterize the remediating function of soil microbiomes and identify the factors that influence their efficiency for remediation. Here, we suggest that soil microbiomes are a promising strategy for soil remediation. Research is now needed to identify how we can manipulate and manage soil microbiomes to improve remediation efficiency and increase soil fertility at the same time. Therefore, this review aims to emphasize the importance of soil microbiomes in bioremediation and promote further development of this strategy into a widely accepted technique.     

Biological Indices for Soil Quality Evaluation: Perspectives and Limitations

Soil quality is threatened by the increase in human population and by the fact that most of the cultivable land is intensively used. The initial interest in this topic focused on defining soil quality but shifted into how to measure soil quality in the late 1990s. There is a general agreement that soil biochemical, microbiological and biological properties are more suitable than physical and/or chemical properties for the purpose of estimating alterations in soil quality and hence soil degradation. To date, most studies have used microbial biomass, soil respiration and enzymatic activities to obtain soil quality indices, whereas less focus has been given to soil fauna (microarthropods and nematodes). This article aims to do a critical review of soil quality indices based on soil biological and biochemical activities, mainly microbial biomass, soil respiration and the activity of several enzymes. Limitations within the database of articles that are focussed on broad scale application of soil quality indices include the difficulty of selecting the highest quality soils for comparison purposes, lack of standardisation of analytical methods, and inclusion of an insufficient number of soil types and ecosystems. There is a need to validate soil quality indices, both, spatially and temporally and to explore the use of indices that integrate faunal and microbial measurements. Copyright © 2013 John Wiley & Sons, Ltd.     

Limitations when quantifying microbial carbon and nitrogen by fumigation‐extraction in rooted soils

Soil microbial C and N (C_mic, N_mic) estimation by the chloroform fumigation‐extraction method is erroneous in densely rooted soils due to CHCl₃‐labile C and N compounds. The effect of a pre‐extraction with 50 mM K₂SO₄ and a pre‐incubation (conditioning at 25 °C for 7 days) on the flush in extractable, CHCl₃‐labile C (C‐flush) and N (N‐flush) was tested with reference to rooting density (0.3—75 mg root dry matter g^—1) in one arable and 3 grassland soils. In the arable soil and in the second horizon (10—20 cm) of a grassland soil, C‐flush values were not affected by the pre‐extraction. However, the pre‐extraction considerably reduced C‐flush values in the top soils of the grassland (above 10 cm). Only about 42 % was found in the pre‐extracted roots and the rest was lost during the pre‐extraction. The estimated concentrations of N_mic decreased due to pre‐extraction of soil samples with low root biomass. Clearly, the concentrations of N_mic were underestimated by introducing the pre‐extraction. Soil pre‐incubation reduced C‐flush values only slightly, whereas N‐flush values were not affected. It can be concluded that (1) CHCl₃‐labile root C and N is partly extracted with K₂SO₄ after pre‐incubation and (2) CHCl₃‐labile C and N removed with the roots during pre‐extraction is partly derived from microbial biomass. Soils with low rooting density (arable soils, grassland soils below approximately 10 cm depth) should therefore be fumigated and extracted without pre‐extraction. In densely rooted soils, fumigation extraction with and without pre‐extraction probably gives estimates for the minimum and maximum of C_mic and N_mic.     

Soil microbial biomass and activity: the effect of site characteristics in humid temperate forest ecosystems

Microbial biomass, respiratory activity, and in‐situ substrate decomposition were studied in soils from humid temperate forest ecosystems in SW Germany. The sites cover a wide range of abiotic soil and climatic properties. Microbial biomass and respiration were related to both soil dry mass in individual horizons and to the soil volume in the top 25 cm. Soil microbial properties covered the following ranges: soil microbial biomass: 20 µg C g^–1–8.3 mg C g^–1 and 14–249 g C m^–2, respectively; microbial C–to–total organic C ratio: 0.1%–3.6%; soil respiration: 109–963 mg CO₂‐C m^–2 h^–1; metabolic quotient (qCO₂): 1.4–14.7 mg C (g C_mic)^–1 h^–1; daily in‐situ substrate decomposition rate: 0.17%–2.3%. The main abiotic properties affecting concentrations of microbial biomass differed between forest‐floor/organic horizons and mineral horizons. Whereas microbial biomass decreased with increasing soil moisture and altitude in the forest‐floor/organic horizons, it increased with increasing N_tot content and pH value in the mineral horizons. Quantities of microbial biomass in forest soils appear to be mainly controlled by the quality of the soil organic matter (SOM), i.e., by its C : N ratio, the quantity of N_tot, the soil pH, and also showed an optimum relationship with increasing soil moisture conditions. The ratio of C_mic to C_org was a good indicator of SOM quality. The quality of the SOM (C : N ratio) and soil pH appear to be crucial for the incorporation of C into microbial tissue. The data and functional relations between microbial and abiotic variables from this study provide the basis for a valuation scheme for the function of soils to serve as a habitat for microorganisms.     

Role of beneficial microbial gene pool in mitigating salt/nutrient stress of plants in saline soils through underground phytostimulating signalling molecules

Soil salinity diminishes soil health and reduces crop yield, which is becoming a major global concern. Salinity stress is one of the primary stresses, leading to several other secondary stresses that restrict plant growth and soil fertility. The major secondary stresses induced in plants under saline-alkaline conditions include osmotic stress, nutrient limitation, and ionic stress, all of which negatively impact overall plant growth. Under stressed conditions, certain beneficial soil microflora ...     

生物炭对土壤可持续健康的影响：探索和热点综述

Biochar as a soil amendment is confronted with the challenge that it must benefit soil health as it can be by no means separated from soils once it is added. The available literature even though sparse and mostly based on short-term studies has been encouraging and the trend obtained so far has raised many hopes. Biochar has been reported to positively impact an array of soil processes ranging from benefiting soil biology, controlling soil-borne pathogens, enhancing nitrogen fixation, improving soil physical and chemical properties, decreasing nitrate (NO₃^-) leaching and nitrous oxide (N₂O) emission to remediation of contaminated soils. However, very little biochar is still utilized as soil amendment mainly because these benefits are yet to be quantified, and also the mechanisms by which the soil health is improved are poorly understood. Due to the infancy of research regarding this subject, there are still more questions than answers. The future research efforts must focus on carrying out long-term experiments and uncover the mechanisms underlying these processes so that key concerns surrounding the use of biochar are addressed before its large scale application is recommended.     

不同施肥和耕作制度下土壤微生物多样性研究进展

本文主要介绍了运用Biolog GN、磷脂脂肪酸(PLFA)、核酸分析法进行土壤微生物群落分析的优缺点,综述了施肥、耕作两种农业措施对土壤微生物多样性影响的研究进展。指出不同施肥处理对微生物影响效果不同,合理施用有机肥有利于维持土壤微生物的多样性及活性;由于受其他环境因素(如土壤类型、农作制度、残茬量等)的影响,不同耕作措施对土壤微生物多样性影响有差异,但是大多试验结果显示免耕、少耕能增加微生物多样性和生物量,保持系统的稳定性。文章还指出了目前研究中存在的问题,并对今后的研究方向做了展望。     

Siderophore-Producing Rhizobacteria as a Promising Tool for Empowering Plants to Cope with Iron Limitation in Saline Soils: A Review

Iron (Fe) bioavailability to plants is reduced in saline soils; however, the exact mechanisms underlying this effect are not yet completely understood. Siderophore-expressing rhizobacteria may represent a promising alternative to chemical fertilizers by simultaneously tackling salt-stress effects and Fe limitation in saline soils. In addition to draught, plants growing in arid soils face two other major challenges:high salinity and Fe deficiency. Salinity attenuates growth, affects plant physiology, and causes nutrient imbalance, which is, in fact, one of the major consequences of saline stress. Iron is a micronutrient essential for plant development, and it is required by several metalloenzymes involved in photosynthesis and respiration. Iron deficiency is associated with chlorosis and low crop productivity. The role of microbial siderophores in Fe supply to plants and the effect of plant growth-promoting rhizobacteria (PGPR) on the mitigation of saline stress in crop culture are well documented. However, the dual effect of siderophore-producing PGPR, both on salt stress and Fe limitation, is still poorly explored. This review provides a critical overview of the combined effects of Fe limitation and soil salinization as challenges to modern agriculture and intends to summarize some indirect evidence that argues in favour of siderophore-producing PGPR as biofertilization agents in salinized soils. Recent developments and future perspectives on the use of PGPR are discussed as clues to sustainable agricultural practices in the context of present and future climate change scenarios.     

黄土高原典型土壤全氮和微生物氮剖面分布特征研究

为阐明黄土高原典型土壤全氮和微生物氮含量随土壤类型、土层和土地利用方式变化规律,研究了从北向南依次分布的干润砂质新成土(神木)、黄土正常新成土(延安)和土垫旱耕人为土(杨陵)等典型土壤的全氮和微生物氮含量的变化特征。结果表明,不同土壤类型、不同土层全氮和微生物氮含量存在显著差异。从南到北,全氮和微生物氮含量显著下降(P0.05)。对同一土壤类型,全氮和微生物氮含量在060.cm随土层深度增加下降很明显,60120.cm有轻微下降,120.cm以下低而稳定。微生物氮含量随土壤类型的变化趋势与全氮完全相同,其与土壤全氮、有机碳及微生物碳含量均存在极显著正相关关系(P0.01)。土壤微生物氮与全氮比值变化在0.42%9～.44%之间。虽然土地利用对土壤全氮和C/N比影响不显著,但却显著影响微生物氮含量和微生物氮与全氮的比值;与农田土壤相比,草地土壤微生物氮含量和微生物氮与全氮比值均明显增加。这一结果说明微生物氮含量和微生物氮与全氮比值更能有效、快速地反映土壤质量的变化。     

Soil microbial biomass C and N changes in relation to forest conversion in the Northwestern Turkey

Tree species differ in their effect on soil development and nutrient cycling. Conversion of beech coppice to pine plantations can alter soil physical and chemical properties, which in turn may have significant impacts on soil microbial biomass C and N (C_mic, N_mic). The major objective of this study was to evaluate soil quality changes associated with the forest conversion in humid NW Turkey. Results from this study showed that levels of soil organic carbon (C_org), total nitrogen (N_t), moisture, C_mic and N_mic under beech coppice were consistently higher but levels of pH, CaCO₃ and EC were lower compared to pine plantation. Differences between the forest stands in C_mic and N_mic were mainly related to the size of the C_org stores in soil and to tree species. In addition, high level of CaCO₃ is likely to reduce pools of soil organic C and possibly even microbial biomass C and N in pine forests. The average C_mic:N_mic ratios were higher in soils under beech coppice than pine plantation, while C_mic:C_org and N_mic:N_t percentages were similar in both forest types. These results revealed the differences in microbial community structure associated with different tree species and the complex interrelationships between microbial biomass, soil characteristics, litter quantity and quality. Copyright © 2008 John Wiley & Sons, Ltd.     

Soil biochemical and microbial indices in wet tropical forests: Effects of deforestation and cultivation

Little information is available about the long‐term effects of deforestation and cultivation on biochemical and microbial properties in wet tropical forest soils. In this study, we evaluated the general and specific biochemical properties of soils under evergreen, semi‐evergreen, and moist deciduous forests and adjacent plantations of coconut, arecanut, and rubber, established by clear felling portions of these forests. We also examined the effects of change in land use on microbial indices and their interrelationships in soils. Significant differences between the sites occurred for the biochemical properties reflecting soil microbial activity. Microbial biomass C, biomass N, soil respiration, N mineralization capacity, ergosterol, levels of adenylates (ATP, AMP, ADP), and activities of dehydrogenase and catalase were, in general, significantly higher under the forests than under the plantations. Likewise, the activities of various hydrolytic enzymes such as acid phosphomonoesterase, phosphodiesterase, casein‐protease, BAA‐protease, β‐glucosidase, CM‐cellulase, invertase, urease, and arylsulfatase were significantly higher in the forest soils which suggested that deforestation and cultivation markedly reduced microbial activity, enzyme synthesis and accumulation due to decreased C turnover and nutrient availability. While the ratios of microbial biomass C : N and microbial biomass C : organic C did not vary significantly between the sites, the ratios of ergosterol : biomass C and ATP : biomass C, qCO2 and AEC (Adenylate Energy Charge) levels were significantly higher in the forest sites indicating high energy requirements of soil microbes at these sites.     

牧场土壤碳、氮和微生物动力学研究:放牧强度和种植方式的影响

Management intensity critically influences the productivity and sustainability of pasture systems through modifying soil microbes, and soil carbon(C) and nutrient dynamics; however, such effects are not well understood yet in the southeastern USA. We examined the effects of grazing intensity and grass planting system on soil C and nitrogen(N) dynamics, and microbial biomass and respiration in a long-term field experiment in Goldsboro, North Carolina, USA. A split-plot experiment was initiated in 2003 on a highly sandy soil under treatments of two grass planting systems(ryegrass rotation with sorghum-sudangrass hybrid and ryegrass seeding into a perennial bermudagrass stand) at low and high grazing densities. After 4 years of continuous treatments, soil total C and N contents across the 0–30 cm soil profile were 24.7% and 17.5% higher at the high than at the low grazing intensity, likely through promoting plant productivity and C allocation belowground as well as fecal and urinary inputs. Grass planting system effects were significant only at the low grazing intensity, with soil C, N, and microbial biomass and respiration in the top 10 cm being higher under the ryegrass/bermudagrass than under the ryegrass/sorghum-sudangrass hybrid planting systems. These results suggest that effective management could mitigate potential adverse effects of high grazing intensities on soil properties and facilitate sustainability of pastureland.     

Ramifications of crop residue loading for soil microbial community composition,activity and nutrient supply

Variable results have been reported on the effects of crop residue loads on soil microbial properties. We investigated changes in soil bacterial composition, β-glucosidase enzyme activity and nutrient bioavailability in response to wheat residue loading. The treatments included three levels of above-ground wheat residues (removed, retained or supplemented), with or without fertilizer N. Bacteroidetes, Firmicutes and Verrucomicrobia (the first two are copiotrophs) were less abundant where residues were removed than where residues were retained or supplemented, but the reverse was true for Actinobacteria, Cyanobacteria, Chloroflexi and Nitrospirae (all oligotrophs, although some Actinobacteria can be copiotrophic). Actinobacteria were also less abundant where fertilizer N was applied, and the abundances of their genera (including Arthrobacter and Mycobacterium) increased where residues were removed, confirming that they were oligotrophic in this study. β-diversity showed similar differences in the bacterial community structures because of residue management, but α-diversity was not affected by residue management or N fertilizer. β-glucosidase enzyme activities increased as C inputs increased with residue manipulation and N fertilizer. The enzyme activities increased with increasing residue loading in the 0–15 cm soil depth, but decreased with soil depth. Soil K supply increased with increasing residue loading, but nitrate-N supply was highest with residue retention. These results demonstrate remarkable resilience of soil microbial functioning under a wide range of crop residue inputs, without adverse effects on enzyme activity attributable to inorganic N fertilizer. The increasing β-glucosidase activity with increasing residue loading probably explains why crop residue return does not always increase soil C stocks.     

Microbial biomass and microbial C:N ratio in bulk soil and buried bags for evaluating in situ net N mineralization in agricultural soils

The in situ net nitrogen mineralization (N_net) was estimated in five agricultural soils under different durations of organic farming by incubating soil samples in buried bags. Simultaneously, soil microbial C and N was determined in buried bags and in bulk soil under winter wheat and after harvest. The aim was to check for variations in soil microbial biomass contents and microbial C:N ratios during the incubation period, and their importance for N_net rates. Microbial C and N contents were highest in soils that had been organically farmed for 41 years, whereas N_net rates were highest in a short‐term organically managed soil that had been under grassland use until 36 years ago. The mean coefficient of variation in the bulk soil for microbial C estimates ranged from 5 to 12 %. Microbial N contents were similar inside buried bags and in the bulk soil at the end of the incubation periods. Under winter wheat during the incubation period until harvest, microbial C contents and microbial C:N ratios (in 10—27 cm depth only) decreased more strongly inside buried bags than in the bulk soil. Following harvest of winter wheat and ploughing, microbial biomass increased while in situ N_net decreased, presumably due to N immobilization. The N_net rates were not correlated with microbial N contents or changes in microbial N contents inside buried bags. At the end of the vegetation period of winter wheat, N_net rates were negatively correlated with microbial C:N ratios. Because these ratios concurrently decreased more inside buried bags than in the bulk soil, the N_net estimates of the buried bag method may differ from the N_net rates in the bulk soil at that time.     

Effects of Epigeic Earthworms on Decomposition of Wheat Straw and Nutrient Cycling in Agricultural Soils in a Reclaimed Salinity Area:A Microcosm Study

Earthworms,one of the most important macroinvertebrates in terrestrial ecosystems of temperate zones,exert important influences on soil functions.A laboratory microcosm study was conducted to evaluate the influence of the earthworm Eisenia fetida on wheat straw decomposition and nutrient cycling in an agricultural soil in a reclaimed salinity area of the North China Plain.Each microcosm was simulated by thoroughly mixing wheat straw into the soil and incubated for 120 d with earthworms added at 3 different densities as treatments:control with no earthworms,regular density(RD)with two earthworms,and increased density(ID)with six earthworms.The results showed that there was no depletion of carbon and nitrogen pools in the presence of the earthworms.Basal soil respiration rates and metabolic quotient increased with the increase in earthworm density during the initial and middle part of the incubation period.In contrast,concentrations of microbial biomass carbon and microbial biomass quotient decreased in the presence of earthworms.Earthworm activity stimulated the transfer of microbial biomass carbon to dissolved organic carbon and could lead to a smaller,but more metabolically active microbial biomass.Concentrations of inorganic nitrogen and NO₃^--N increased significantly with the increase in earthworm density at the end of the incubation(P<0.05),resulting in a large pool of inorganic nitrogen available for plant uptake.Cumulative net nitrogen mineralization rates were three times higher in the ID treatment than the RD treatment.