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.
Soil biota is the living component of soil organic matter (SOM), and plays a key role in the decomposition of SOM. Both soil biota and SOM are indicators of soil fertility and soil quality. However, they both are sensitive to soil disturbance. Although researchers developed various technologies to detect soil biota and SOM, they are mostly destructive and cause disturbance to soil, which may not reflect the actual situation of soil biota and SOM. Therefore, here we mostly focused on the non-destructive physical methods for estimating soil biota and SOM and discussed their advantages and disadvantages. These methods include but not limited to acoustic detection, radio frequency identification, radioactive tagging, hyperspectral sensing and electron energy loss spectroscopy. In addition, we pointed out the current research problems and the potential research directions for applications of physical methods in estimation of soil biota and SOM.
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.
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.