Soil is inhabited by a myriad of microorganisms, many of which can form supracellular structures, called biofilms, comprised of surface-associated microbial cells embedded in hydrated extracellular polymeric substance that facilitates adhesion and survival. Biofilms enable intensive inter- and intra-species interactions that can increase the degradation efficiency of soil organic matter and materials commonly regarded as toxins. Here, we first discuss organization, dynamics and properties of soil biofilms in the context of traditional approaches to probe the soil microbiome. Social interactions among bacteria, such as cooperation and competition, are discussed. We also summarize different biofilm cultivation devices in combination with optics and fluorescence microscopes as well as sequencing techniques for the study of soil biofilms. Microfluidic platforms, which can be applied to mimic the complex soil environment and study microbial behaviors at the microscale with high-throughput screening and novel measurements, are also highlighted. This review aims to highlight soil biofilm research in order to expand the current limited knowledge about soil microbiomes which until now has mostly ignored biofilms as a dominant growth form.

The soil microbial carbon pump (MCP) conceptualizes a sequestration mechanism based on the process of microbial production of a set of new organic compounds, which carry the carbon from plant, through microbial anabolism, and enter into soil where it can be stabilized by the entombing effect. Understanding soil MCP and its related entombing effect is essential to the stewardship of ecosystem services, provided by microbial necromass in the formation and stabilization of soil organic matter as well as its resilience and vulnerability to global change. The mechanism and appraisal of soil MCP, however, remain to be elucidated. This lack of knowledge hampers the improvement of climate models and the development of land use policies. Here, I overview available knowledge to provide insights on the nature of the soil MCP in the context of two main aspects, i.e., internal features and external constraints that mechanistically influence the soil MCP operation and ultimately influence microbial necromass dynamics. The approach of biomarker amino sugars for investigation of microbial necromass and the methodological limitations are discussed. Finally, I am eager to call new investigations to obtain empirical data in soil microbial necromass research area, which urgently awaits synthesized quantitative and modeling studies to relate to soil carbon cycling and climate change.

Archaeal and bacterial ammonia-oxidizers drive the first step of nitrification, ammonia oxidation. Despite their importance, the relative contribution of soil factors influencing the abundance, diversity and community composition of ammonia oxidizing archaea (AOA) and bacteria (AOB) are seldom compared. In this study, the AOA and AOB communities in soils from a long-term fertilization experiment (which formed gradients of pH and nutrients) were measured using 454 pyrosequencing of the amoA gene. Results showed that both AOA and AOB communities were influenced by fertilization practice. Changes of AOA abundance, diversity and community structure were closely correlated with a single factor, soil pH, and the abundance and diversity of AOA were lower under the acidified treatments. By contrast, AOB abundance was higher in the acidified soil than in the control soil while AOB diversity was little impacted by soil acidification, and both the abundance and diversity of AOB were most highly correlated with soil carbon and available phosphorus. These results indicated that AOB diversity seemed more resistant to soil acidification than that of AOA, and also suggested that AOB have greater ecophysiological diversity and broader range of habitats than AOA in this lime concretion black soil, and the potential contribution of AOB to ammonia oxidation in acid environments should not be overlooked.

Long-term application of chemical fertilizers causes soil degradation and nitrogen (N) loss, but these effects could be alleviated by organic fertilizers. In addition, crop rotation is a feasible practice to increase soil fertility, soil quality and crop yields comparing with monocultural cropping patterns. However, questions remain concerning how the soil microbiome responds to different manure application rates under crop rotations. Here, we collected soil samples from a rice-rape system to investigate the response of the soil microbiome to nine years of pig manure application at different rates (CK: 0 kg ha^-1, M1: 1930 kg ha^-1, M2: 3860 kg ha^-1 and M3: 5790 kg ha^-1). Our results revealed that the bacterial α-diversity (Chao1 and Shannon index) in the rape season increased first and then decreased with increasing manure application rates, and a high manure load tended to decrease the bacterial α-diversity in the rice season. Long-term manure application enriched some copiotrophic bacteria, such as Proteobacteria and Actinobacteria, while it decreased the relative abundance of Nitrospirae. Redundancy analysis (RDA) and the Mantel test indicated that soil pH, TC, TN, AP, C/P and N/P ratios were the main factors influencing bacterial communities. Moreover, network analysis showed that a low manure application rate shaped a complexly connected and stable bacterial community, while higher manure application rate decreased the stability of the bacterial network. These findings improve our understanding of bacterial responses to long-term manure application under crop rotations and their relationships with soil factors, especially in the context of increasing fertilizer inputs.

Although soil nematode diversity has been used as an indicator of habitat characteristics and environmental change, the diversity of entire soil nematode communities has not been comprehensively evaluated at different taxonomic levels, or for different functional groups, or at a fine taxonomic level within functional groups. In this study, two taxonomic diversity indices, the Shannon-Wiener index (H′) and Simpson index (l), were used to evaluate the following: 1) nematode diversity at different taxonomic levels for the whole community, 2) nematode diversity of different functional groups, and 3) nematode generic diversity of functional groups in the following four land-use types: forage land, cropland, secondary forest, and grass-shrubland. The results showed that significant differences in nematode diversity among land-use types were detected by assessment at the order level but not at the family or genus level. The results also showed that significant differences in nematode diversity were better revealed by assessment of trophic groups rather than cp groups. The generic diversities (H′) of omnivorous nematodes and cp3 nematodes also significantly differed among land-use types. Our results indicate that diversity at a high taxonomic level (i.e., order) may be a more useful indicator than diversity at a low taxonomic level (i.e., family or genus) of differences among land-use types. In addition, the functional group diversity (i.e., trophic group, cp group, and the combination of these two groups) for the whole community and the taxonomic diversity within functional groups were useful indicators of differences among land-use types.

Global warming leads to deglaciations in high-elevation regions, which exposes deglaciated soils to microbial colonization. Disparity in year-to-year successional patterns of bacterial community and influencing factors in freshly deglaciated soils remain unclear. We explored the abundance of bacterial 16S rRNA gene and community succession in deglaciated soils along a 14-year chronosequence after deglaciation using qPCR and Illumina sequencing on the Tibetan Plateau. The results showed that the abundance of bacterial 16S rRNA gene gradually increased with increasing deglaciation age. Soil bacterial community succession was clustered into three deglaciation stages, which were the early (zero-year old), transitional (1–7 years old) and late (8–14 years old) stages. A significantly abrupt bacterial community succession occurred from the early to the transitional stage (P<0.01), while a mild succession (P = 0.078) occurred from the transitional to the late stage. The bacterial community at the early and transitional stages were dominated by Proteobacteria, while the late stage was dominated by Actinobacteria. Less abundant (<10%) Acidobacteria, Gemmatimonadetes, Verrucomicrobia, Chloroflexi, Planctomycetes, unclassified bacteria dominantly occurred in the transition and late stage and Cyanobacteria in the early stage. Total organic carbon (24.7%), post deglaciation age (21%), pH (16.5%) and moisture (10.1%) significantly contributed (P<0.05) to the variation of bacterial community succession. Our findings provided a new insight that short time-scale chronosequence is a good model to study yearly resolution of microbial community succession.

Arbuscular mycorrhizal (AM) fungi are ubiquitous soil fungi that readily form symbiotic associations with most terrestrial plants. The growth and functions of AM fungi depend on carbohydrates supplied by the plants, in return, they assist the plants acquire mineral nutrients (e.g., phosphorus) from soil. The AM symbiosis also improves plant survival in various environments of unfavorable growth conditions, such as metal (loid) contaminated soil. It has been well demonstrated that AM symbiosis improved plant adaptation to Cr contaminated soil, which would have a great potential in phytoremediation and ecological restoration of Cr contaminated soils. By using Cr as an example case, we have reviewed the role of AM fungi in alleviation of Cr phytotoxicity and associated factors influencing AM plant Cr tolerance. AM symbiosis improves plant Cr tolerance through its direct roles in Cr stabilization and transformation and indirect roles via AM symbiosis mediated nutrient acquisition and physiological regulation. Future research perspectives on physiological and molecular mechanisms underlying Cr behavior and detoxification in AM symbiosis, as well as potential usage of AM fungi in ecological restoration and agriculture production in Cr contaminated soils were also proposed.

• Elevated CO₂ increased the amounts of rhizodeposits.

Rhizodeposits in rice paddy soil are important in global C sequestration and cycling. This study explored the effects of elevated CO₂ and N fertilization during the rice growing season on the subsequent mineralization and retention of rhizodeposit-C in soil aggregates after harvest. Rice (Oryza sativa L.) was labeled with ¹³CO₂ under ambient (400 ppm) and elevated (800 ppm) CO₂ concentrations with and without N fertilization. After harvest, soil with labeled rhizodeposits was collected, separated into three aggregate size fractions, and flood-incubated for 100 d. The initial rhizodeposit-¹³C content of N-fertilized microaggregates was less than 65% of that of non-fertilized microaggregates. During the incubation of microaggregates separated from N-fertilized soils, 3%–9% and 9%–16% more proportion of rhizodeposit-¹³C was mineralized to ¹³CO₂, and incorporated into the microbial biomass, respectively,, while less was allocated to soil organic carbon than in the non-fertilized soils. Elevated CO₂ increased the rhizodeposit-¹³C content of all aggregate fractions by 10%–80%, while it reduced cumulative ¹³CO₂ emission and the bioavailable C pool size of rhizodeposit-C, especially in N-fertilized soil, except for the silt-clay fraction. It also resulted in up to 23% less rhizodeposit-C incorporated into the microbial biomass of the three soil aggregates, and up to 23% more incorporated into soil organic carbon. These results were relatively weak in the silt-clay fraction. Elevated CO₂ and N fertilizer applied in rice growing season had a legacy effect on subsequent mineralization and retention of rhizodeposits in paddy soils after harvest, the extent of which varied among the soil aggregates.

Soil nematodes are the most numerous components of the soil fauna in terrestrial ecosystems. The occurrence and abundance of nematode trophic groups determine the structure and function of soil food webs. However, little is known about how nitrogen deposition and land-use practice (e.g. mowing) affect soil nematode communities. We investigated the main and interactive effects of nitrogen addition and mowing on soil nematode diversity and biomass carbon in nematode trophic groups in a temperate steppe in northern China. Nitrogen addition and mowing significantly decreased the abundance of soil nematodes and trophic diversity but had no effects on nematode richness and the Shannon-Wiener diversity. Nitrogen addition influenced soil nematode communities through decreasing soil pH. Mowing influenced soil nematode communities through decreasing soil moisture. Nitrogen addition enhanced the bacterial energy channel but mowing promoted fungal energy channel in the soil micro-food web. Our study emphasizes that ecosystem function supported by soil organisms can be greatly influenced by nitrogen deposition, and mowing cannot mitigate the negative effects of nitrogen deposition on soil food webs.

• We evaluated effects of fungi on N₂O emission in Chinese milk vetch-containing soils.

Fungi play an important role in soil nitrous oxide (N₂O) emission in many agricultural soil systems. However, the effect of fungi on N₂O emission in Chinese milk vetch (CMV)-containing soils has not been examined sufficiently. This study investigated the contribution of bacteria and fungi to soil N₂O emission in CMV-amended soils. We compared soils from an experimental field in the Fujian Academy of Agricultural Sciences that had been treated with 30 000 kg of CMV per 667 m² per year with one that was not treated with CMV. We incubated soil using cycloheximide and streptomycin to differentiate fungal and bacterial N₂O emissions, respectively. Quantitative PCR (qPCR) was performed to investigate bacterial and fungal abundances in the two agricultural soil ecosystems. The contribution of fungi to soil N₂O emission in CMV-amended soils was greater than that in non-CMV-amended paddy soils, with fungi accounting for more than 56% of the emissions in CMV-amended soils. Quantitative PCR showed that the ratio of the internal transcribed spacer to 16S rDNA was significantly higher in CMV-amended soils than in non-CMV-amended paddy soils. Furthermore, soil properties, such as pH (P<0.05) and NH₄⁺ concentration (P<0.05), significantly and negatively affected N₂O emission by fungi in soil, whereas the total organic carbon (P<0.05) and NO₃^- concentration (P<0.05) showed significant positive effects. Fungi may be important contributors to N₂O production in CMV-amended soils, which may create challenges for mitigating N₂O production.

• Straw returning significantly affects silicon fraction transformation;

Returning crop straw into the soil is an important practice to balance biogenic and bioavailable silicon (Si) pool in paddy, which is crucial for the healthy growth of rice. However, owing to little knowledge about soil microbial communities responsible for straw degradation, how straw return affects Si bioavailability, its uptake, and rice yield remains elusive. Herein, we investigate the change of soil Si fractions and microbial community in a 39-year-old paddy field amended by a long-term straw return. Results show that rice straw return significantly increased soil bioavailable Si and rice yield from 29.9% to 61.6% and from 14.5% to 23.6%, respectively, when compared to NPK fertilization alone. Straw return significantly altered soil microbial community abundance. Acidobacteria was positively and significantly related to amorphous Si, while Rokubacteria at phylum level, Deltaproteobacteria, and Holophagae at class level was negatively and significantly related to organic matter adsorbed and Fe/Mn-oxide-combined Si in soils. Redundancy analysis of their correlations further demonstrated that Si status significantly explained 12% of soil bacterial community variation. These findings suggest that soil bacteria community and diversity interact with Si mobility by altering its transformation, thus resulting in the balance of various nutrient sources to drive biological Si cycle in agroecosystem.

Dissimilarity nitrate reduction to ammonium (DNRA) is of significance in agriculture ecosystems as the process is beneficial to N retention in soils. However, how fertilization regimes influence DNRA rates and functional microbes in agriculture was rarely estimated. In the present study, a 2-year pot experiment was conducted in two contrasting paddy soils to evaluate the effects of straw and nitrogen addition on DNRA process and the related functional microbes, using stable isotope tracer and molecular ecology techniques. The results showed that the abundance and transcription activity of nitrite reductase encoding gene (nrfA) involved in DNRA process and DNRA rates were significantly higher in alkaline soils than in acidic soils. Straw incorporation significantly enhanced nrfA gene abundance and transcription activity, with a greater effect in alkaline soil than in acidic soil. The rates of DNRA, abundance and transcription activity of nrfA gene positively correlated to soil C/N and C/NO₃⁻ induced by straw application. Sequencing analysis based on nrfA gene transcript showed that Deltaproteobacteria was the most dominant group in both soil types (30.9%-67.4%), while Gammaproteobacteria, Chloroflexi, Actinobacteria were selectively enriched by straw incorporation. These results demonstrated that DNRA activity can be improved by straw return practice in paddy soils while the effect will vary among soil types due to differentiated functional microbial communities and edaphic properties.

The mutual interdependence of plants and arbuscular mycorrhizal fungi (AMF) is important in carbon and mineral nutrient exchange. However, an understanding of how AMF community assemblies vary in different forests and the underlying factors regulating AMF diversity in native tropical forests is largely unknown. We explored the AMF community assembly and the underlying factors regulating AMF diversity in a young (YF) and an old-growth forest (OF) in a tropical area. The results showed that a total of 53 AMF phylogroups (virtual taxa, VTs) were detected, 38±1 in the OF and 34±1 in the YF through high-throughput sequencing of 18S rDNA, and AMF community composition was significantly different between the two forests. A structural equation model showed that the forest traits indirectly influenced AMF diversity via the plant community, soil properties and microbes, which explained 44.2% of the total observed variation in AMF diversity. Plant diversity and biomass were the strongest predictors of AMF diversity, indicating that AMF diversity was dominantly regulated by biotic factors at our study sites. Our study indicated that forest community traits have a predictable effect on the AMF community; plant community traits and soil properties are particularly important for determining AMF diversity in tropical forests.

1. Basic principles of microfluidics are introduced

Microfluidics confers unique advantages in microbiological studies as these devices can accurately replicate the micro- and even nano-scale structures of soil to simulate the habitats of bacteria. It not only helps us understand the spatial distribution of bacterial communities (such as biofilms), but also provides mechanistic insights into microbial behaviors including chemotaxis and horizontal gene transfer (HGT). Microfluidics provides a feasible means for real-time, in situ studies and enables in-depth exploration of the mechanisms of interactions in the soil microbiome. This review aims to introduce the basic principles of microfluidic technology and summarize the recent progress in microfluidic devices to study bacterial spatial distribution and functions, as well as biological processes, such bacterial chemotaxis, biofilm streamers (BS), quorum sensing (QS), and HGT. The challenges in and future development of microfluidics for soil microbiological studies are also discussed.

Rapid litter turnover in tropical forests and during summer seasons might be due to increases in ligninolytic enzyme activities during warmer periods. We compared ligninolytic enzyme activity [lignin peroxidase (LiP), manganese peroxidase (MnP), and laccase (Lac)] in the organic layers of forest soils across a global climate gradient. As expected, MnP activities in fresh litter layers increased with increasing air temperature. Litter Mn/lignin ratios correlate positively with MnP activity and more rapid litter turnover in warmer climates. In contrast, LiP and Lac activities are regulated by site-specific conditions. Lac activity is commonly observed in less acidic fresh litter layers, while LiP activity localizes in acidified and lignin-rich deeper organic layers. The widespread occurrence of MnP and an increase in MnP activities in warmer climates support efficient lignin degradation in the tropics and during summer seasons. High Mn/lignin ratios in fresh litter could be an indicator of lignin degradability by MnP-producing fungi across global climate gradients.

• This study reviewed the sorption of sex hormones onto soils and sediment.

Sex hormones are a group of potent endocrine disruptors that can be released into agricultural soils and sediment via wastewater discharge and manure fertilization. Sorption represents a critical determinant for the transport potential and risks of sex hormones in the environment. Therefore, this study reviewed the sorption and desorption mechanisms of sex hormones in soil- and sediment-water systems, and summarized the effects of various factors on sorption and desorption processes. A total of 359 set of sorption data were collected from the literature. Sex hormones were mostly described by the linear model. The sorption magnitudes (logK_oc) of estrogens, androgens, and progestins were in the range of 2.77–3.90, 2.55–4.18, and 2.61–4.39, respectively. The average logK_oc values of the sex hormones were significantly correlated with their logK_ow values (R²= 0.13, p<0.05), while the R² values were much lower than those when fewer sex hormones were included for analysis. In addition, the K_d values of most sex hormones were significantly correlated with the OC% of soils and sediment (R²= 0.16−0.99, p<0.05), but were insignificantly correlated with the particle size distribution and surface area. These results indicated that hydrophobic partitioning interaction and other specific interactions are responsible for sex hormone uptake in soil- and sediment-water systems. The sorption of sex hormones in soil- and sediment-water systems can also be affected by other environmental variables, including pH, temperature, and ionic strength. Future studies should focus on the coupled leaching-sorption processes in manure-water-soil systems under field-scale conditions.

• Volcanic inputs and grazing impact the distribution of microbes in Serengeti soil.

As one of the last remaining naturally grazed ecosystems on Earth, the Serengeti National Park is an ideal location to study the influence of migratory mammals on the structure of microbial communities and the factors that generate biogeography of soil microbes. Furthermore, volcanic inputs generate environmental gradients that may also structure microbial communities. We studied 16S rRNA amplicons in a 13-year herbivore removal experiment to examine the influence of grazing and environmental gradients on the natural distribution of soil microbes. Removal of mammalian herbivores shifted microbial community structure, with 31 taxa that were significant indicator taxa of the ungrazed treatment and three taxa that were indicators of the grazed treatment. The abundance of many taxa were correlated with soil texture, phosphorus, iron, calcium and rainfall, and the evenness of taxa within samples was also correlated with these variables. Bayesian general linear mixed effects models with single predictors of multiple, highly correlated variables of beta diversity were consistent with a significant, but weak (2%), effect of grazing, and stronger effects of phosphorus (14%). Beta diversity of microbial communities was greater in grazed than in ungrazed plots; suggesting that the impacts of grazing on community assembly of microbes results from deterministic environmental filtering caused by the influence of herbivores on plant communities and soil properties rather than stochastic dispersal via herds of large mammals. These herbivore effects are superimposed on deterministic environmental filtering by natural soil and precipitation gradients across the Serengeti.

• Microplastics and phthalate acid esters concentrations are positively correlated in soils.

Microplastics (MPs) and Phthalate acid esters (PAEs) co-occur as emerging contaminants of global importance. Their abundance in soil is of increasing concern as plastic-intensive practices continue. Mulching with plastic films, inclusion in fertilizers, composts, sludge application, and wastewater irrigation are all major and common sources of MPs and PAEs in soil. Here, we review studies on the concentration and effects of MPs and PAEs in soil. While there is limited research on the interactions between MPs and PAEs in agroecosystems, there is evidence to suggest they could mutually affect soil ecology and plant growth. Therefore, we propose new research into 1) establishing an efficient, accurate, and simple method to quantify different types of microplastics in soils and plants; 2) exploring the behavior and understanding the mechanisms of co-transfer, transformation, and interactions with soil biota (especially in vegetable production systems); 3) assessing the risk and consequences of combined and discreet impacts of MPs and PAEs on plants and soil biota, and 4) preventing or reducing the transfer of MPs and PAEs into-and within- the food chain.

• Topsoil diversity was greater in phenosoils than genosoils, but the trend was reversed in subsoils.

Human disturbances to soils can lead to dramatic changes in soil physical, chemical, and biological properties. The influence of agricultural activities on the bacterial community over different orders of soil and at depth is still not well understood. We used the concept of genoform and phenoform to investigate the vertical (down to 1 m depth) soil bacterial community structure in paired genosoils (undisturbed forests) and phenosoils (cultivated vineyards) in different soil orders. The study was conducted in the Hunter Valley area, New South Wales, Australia, where samples were collected from 3 different soil orders (Calcarosol, Chromosol, and Kurosol), and each soil order consists of a pair of genosoil and phenosoil. The bacterial community structure was analyzed using high-throughput sequencing of 16S rRNA. Results showed that bacterial-diversity decreased with depth in phenosoils, however, the trend is less obvious in genoform profiles. Topsoil diversity was greater in phenosoils than genosoils, but the trend was reversed in subsoils. Thus, cropping not only affected topsoil bacteria community but also decreased its diversity in the subsoil. Bacterial community in topsoils was influenced by both soil orders and soil forms, however, in subsoils it was more impacted by soil orders. Constrained Analysis of Principal Coordinates revealed that cropping increased the similarity of bacterial structures of different soil orders. This study highlighted the strong influence of agricultural activities on soil microbial distribution with depth, which is controlled by soil orde