Large volumes of liquid water transiently existed on the surface of Mars more than 3 billion years ago. Much of this water is hypothesized to have been sequestered in the subsurface or lost to space. We use rock physics models and Bayesian inversion to ...

The biodiversity of soil animals (fauna) is large, and fauna critically affect soil processes by feeding and fragmenting plant materials and organic substrates. Soil fauna exist in food webs, with a range of feeding modes (trophic levels). Soil faunal biodiversity involves degrees of functional specialization. Soil fauna body size affects soil processes across a broad spatial range: (1) "micro-food webs" with microbes and their protist and nematode predators; (2) microarthropods and enchytraeids, fragmenting decomposing litter; and (3) "ecosystem engineers," e.g., earthworms, termites, and ants, which alter soil physical structure and influence rates of nutrient flows. We consider the conjoint action of the major faunal groups and discuss their roles in ecosystem function worldwide and in the context of ongoing global climate change.

“Leaders stand on the shoulders of those who came before them” (paraphrased from Bernard of Chartres and Isaac Newton among others) and they depend on those around them to hold them up. The evolution of ecosystem science is traced in this chapter from its conceptual beginnings in the late 1500s (and earlier) until now. The importance of “giants” in soil science, botany, chemistry, zoology, and microbiology in establishing the scientific basis for what later would become “ecology” and later yet “ecosystem science” is emphasized. As the science evolved toward the study of the structure and functioning of ecosystems, relying heavily on the systems ecology paradigm and especially as humans became recognized as integral parts thereof, research philosophy and methodology needed to change. Science needed to evolve from individual scientists (giants) with reductionist perspectives to transdisciplinary and interdisciplinary teams of scientists with leaders (often multiple leaders) having holistic, systems thinking perspectives buttressed by cadres of collaborators and technical and administrative supporters, often from many locations nationally and internationally. Now teams are beginning to include social sciences, economists, education and engagement specialists, managers, decision-makers, and other stakeholders.

As a temperature-sensitive transition zone, the subtropical alpine region responds quickly to global warming. However, little is known about soil microbial communities at the treeline, where changes in vegetation in response to global warming are anticipated. Barcoded pyrosequencing of the 16S rRNA gene was used to investigate the bacterial communities of coniferous forest and grassland soils at the treeline of four different peaks above 3,000 m a.s.l. Although the forest soils were more acidic than the grassland soils, the other soil properties were highly variable with no consistent pattern in C and N contents and microbial biomass between two vegetation types. The Acidobacteria and alpha-Proteobacteria were the most abundant phylogenetic groups, although their relative abundances differed among the forest and grassland soil communities and between sites. The composition of bacterial communities or beta-diversity, varied significantly between the sites and vegetation types. In contrast, alpha-diversity only differed significantly between sites. Two of the grassland sites and one forest had converted from forests and grassland, respectively within the last 60 years. The abundances of some genera, such as Acidobacteria Gp2 in the grasslands converted from forests, more closely resembled those of the other forest sites than the historically grassland sites, while the abundance of Acidobacteria Gp1 in the forest converted from grassland was more similar to the historically grassland sites. These results suggest a legacy effect for the transition of forest to grassland. Bacterial community structure also correlated significantly with soil pH, organic C and C/N. These results suggest that the present vegetation at the treeline influences soil bacterial community structure, although there is also a significant legacy effect on the abundance of certain bacterial groups.

We offer a wide range of laboratory and field exercises in soil ecology. First, we consider root-related studies, including rhizotrons and mini-rhizotrons, sequential sampling of root cores, and root ingrowth. Process-related studies are consider next, including soil respiration, and litter decomposition. Soil microbe and protozoan exercises are considered next: quantifying mycorrhizal fungal colonization of roots, analyses for soil microbial biomass, and field exercises for soil protozoan activity and biodiversity. We then consider nematode sampling and extraction. This is followed by sampling and enumeration of microarthropods (mites and collembola). This is followed by quantifying the numbers and biomass of microarthropods. Sampling and enumeration of enchytraeids is presented next. This is concluded with methods for sampling and quantifying earthworms, followed by an exercise for conjoint sampling of macroinvertebrates, namely arthropods and earthworms.

We focus on the future effects of soil biotas and soil processes on Global Climate Change. This includes changes in evolution and uptake of the principal greenhouse gases and their interplay with pools of labile and resistant soil organic matter. The full costs of ecosystem services, as human population pressure increases, require innovative thinking and research. Simulation models provide insights and uncertainties in soil-atmosphere-biosphere fluxes. Soil biodiversity changes driven by global change are the result of direct impacts (changes in temperature and moisture), and indirectly, through shifts in nutrient supply from plants. Invasive plants and animals add to the complexity of these long-term processes. Future studies of land-use management will encompass the fact that soil biota act in concert to provide multiple benefits. Increasing food web complexity in soils should provide improved “health” (i.e., enhanced recycling of nutrients) in agro-ecosystems. We conclude with a critique of the interfaces between soil food webs, ecosystem engineers, and enhanced provision of ecosystem services over landscapes at millennial time scales.

A functional approach in soil ecology focuses on integrating variables in soils. These variables include: decomposition rates, nutrient dynamics, soil respiration, and formation of soil structure. These generalized measurements summarize and integrate the combined actions of soil microflora and fauna, as influenced by abiotic variables and resource quality factors.

Inputs from primary production in soils are from two principal sources: aboveground and belowground. We focus on inputs from roots and their rhizosphere associates, including mycorrhiza and rhizobia. Input measurement techniques include various nondestructive techniques, including rhizotrons and minirhizotrons, and destructive techniques, including soil coring, and isotopic-labeling of roots, followed by destructive sampling at specified time intervals to determine dynamics, e.g., over an entire growing season. Of equal importance to roots themselves are their generally more efficient physiological extensions, the root-fungus mutualistic association, mycorrhiza. At a cost of 5%–30% of the total photosynthate translocated belowground, mycorrhiza assists in obtaining inorganic nutrients, water, and in some cases, organic nutrients over a much wider range of the soil volume than roots alone. This symbiotic association has a significant effect on other biota, namely microbes and fauna, which inhabit all soil systems. Long-term Free Air Carbon Enrichment (FACE) studies have yielded information on flows to roots and their species-rich grazers and microbial and faunal associates.

Food web ecology has the potential as an integrating concept to unify perspectives in above-ground and below-ground ecology. A typical food web, particularly in arid lands, has 7–8 membered food chains embedded in the food web. By viewing soil systems holistically, including such microfauna as protists, and mesofauna (nematodes), there are ample supplies of biota (food) to enable longer food chains to exist. Thus production efficiencies can be up to 70%. Trophic transfer efficiencies, often thought of as maximal at 10%, can be up to 20%, particularly in such soil “hot spots” as rhizospheres and drilospheres. The future of food web ecology research is bright, with conjoint studies of biodiversity and including a wide range of innovative isotopic tracer techniques.

Reforestation with different tree species could alter soil properties and in turn affect the bacterial community. However, the effects of long-term reforestation on bacterial community structure and diversity of subtropical forest soils are poorly understood. In the current study, we applied error-corrected barcoded pyrosequencing to characterize the differences in the soil bacterial community in a low mountain, subtropical forest subjected to reforestation. The communities were sampled in the summer and winter from a native broadleaved forest (BROAD-Nat) and two adjacent coniferous plantations, a Calocedrus formosana forest of 80 years (CONIF-80) and a Cunninghamia konishii forest of 40 years (CONIF-40). The soil bacterial communities among three forest types were dominated by Acidobacteria and Alphaproteobacteria. The distribution of abundant genera among communities was different. Based on the Shannon diversity index, the bacterial alpha diversity of CONIF-40 community was significantly higher than that in the CONIF-80 and BROAD-Nat soils. In both of the coniferous plantations, the soil bacterial diversity in summer was also higher than that in winter. Distribution of some abundant phylogenetic groups, K-shuff and redundancy analysis of beta diversity among communities showed that the bacterial structure of three soil communities differed between two seasons. These results suggest that seasonal differences influence the diversity and structure of bacterial soil communities and that the communities remain different even after a long period of reforestation.

We set the stage by giving four main reasons to study soils: (1) humanity depends upon soils for their livelihood and ecosystem services; (2) as a last frontier in biodiversity research, soils teem with common and rare organisms; (3) soils are an excellent medium to study ecology ranging from organisms to ecosystems and entire regions; (4) more importantly, soils are exciting, challenging, and fun! We present a historical background of soil concepts, extending from early Chinese and Mesopotamian cultures, through Greco-Roman, into modern times. Much modern research focuses at the interface between soil–water–gases and organisms. Soils have texture and structure, arising via a range of mechanisms, mediated by the production of soil organic matter. The hierarchical nature of soil structure leads to characteristic profiles, developing over time. The historical nature of soils extends to including “libraries” of DNA. We conclude with an introduction to soils in their provision of ecosystem services, a major theme for the entire book.

The badland soils originated from mudstone in southwestern Taiwan are inhospitable for plant growth because of their high‐salinity and poor physicochemical properties. Thorny bamboo is one of the few plants that can survive in these soils. To investigate the responses of the soil bacterial communities to plant cover, bare soils and soils from thorny bamboo plantations were analyzed with the barcoded pyrosequencing technique. Actinobacteria and Proteobacteria predominated in the bare soil communities, but Acidobacteria , Actinobacteria , and Proteobacteria were the most abundant groups in the thorny bamboo soils. Environmental stress may have selected for Actinobacteria in the bare community. Canonical correspondence analysis of the distributions of abundant operational taxonomic units also revealed consistent differences between the communities in the bamboo and bare soils. The bacterial diversity in the bamboo soils was also higher than that in the bare soils. The soluble organic carbon and nitrogen in bamboo soils were significantly higher, but electrical conductivity was lower than that in the bare soils. These soil properties, as well as soil pH, were related to the structure and diversity of the bacterial communities. Statistical analyses also indicated that these factors affected the distribution of Acidobacteria , Actinobacteria , Alphaproteobacteria , and Gammaproteobacteria . Analysis of thiocyanate oxidation activity revealed higher activity in the bare than in the bamboo soils, further suggesting differences in structure and metabolic activity between bamboo and bare soil microbial communities. Apparently, growth of thorny bamboo in the badland soil changed soil properties, which in turn directly and/or indirectly affected soil bacterial structure and diversity.

Afforestation results in changes of vegetation and soil properties, which in turn could affect the soil bacteria that play critical roles in the biogeochemical cycles in forest ecosystems. Therefore, the objective of this study was to elucidate the impacts of afforestation on soil bacterial communities. Using the barcoded pyrosequencing technique, the phylogenetic structure and diversity of the soil bacterial communities in moso bamboo and Japanese cedar plantations were compared with that of an adjacent natural hardwood forest. A total of 43,097 bacterial pyrosequences were obtained from soil samples. The majority of these sequences were classified as either Acidobacteria or alpha-Proteobacteria, but the relative abundance of Acidobacteria in bamboo soils was much lower than that in the other two communities. The sequences related to the a-Proteobacteria were dominated by the orders Rhizobiales and Rhodospirillales and were more abundant in the bamboo community. Nonmetric multidimensional scaling analysis of the operational taxonomy units (OTUs) and the distribution of some of the most abundant OTUs revealed distinct bacterial community structures among the three sites. These differences were correlated to soil acidity and C/N ratio, with soil acidity affecting the distribution of Acidobacteria, Actinobacteria, alpha- and beta-Proteobacteria. Based on Shannon diversity indices and richness and rarefaction analyses, the diversity of soil communities decreased in the order bamboo plantation > cedar plantation > hardwood forest. These findings suggest that afforestation and subsequent management of a natural hardwood forest causes differences in soil bacterial community structure and increases in diversity. (C) 2017 Elsevier B.V. All rights reserved.

The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia - Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia.The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise.

Soils are a haven for many phyla of countless numbers of microbes and fauna. The trophic (feeding) interactions between them provide much of the ecological stability of soil systems. Within the web of soil fauna, interactions occur via numerous biogeochemical cycles of the major nutrients, including carbon, nitrogen, phosphorus, and sulfur. These cycles are in turn influenced by aboveground and belowground interactions of plants and biota. Recent studies point to the considerable positive effects of the diversity of the soil fauna on rates of decomposition in a wide range of ecosystems worldwide. Awareness of soil biodiversity provides additional support for the influence of soil microbes and fauna on enhancing soil quality and supporting the recycling of nutrients in soils.

Soils may be viewed as the organizing centers for terrestrial ecosystems. This is largely the result of organismal activities in the soil. Major functions such as ecosystem production, respiration, and nutrient recycling are controlled by the rates at which nutrients are released by decomposition in the soil and litter horizons. The array of biota, including microbes, microbe-feeding fauna, vegetation, and consumers are all influenced by soil processes, and the organisms in turn have an impact on the soil system.