Tree indiscernibilities, revisited

We give definitions that distinguish between two notions of indiscernibility for a set \{a_\eta \mid \eta \in \W\} that saw original use in \cite{sh90}, which we name \textit{\s-} and \textit{\n-indiscernibility}. Using these definitions and detailed proofs, we prove \s- and \n-modeling theorems and give applications of these theorems. In particular, we verify a step in the argument that TP is equivalent to TP$_1$ or TP$_2$ that has not seen explication in the literature. In the Appendix, we exposit the proofs of \citep[{App. 2.6, 2.7}]{sh90}, expanding on the details.Comment: submitte

Enhancing Biodiversity and Multifunctionality of an Organic Farmscape in California’s Central Valley

Organic farmers in the USA increasingly manage the margins of previously monocultured farmed landscapes to increase biodiversity, e.g. they restore and protect riparian corridors, plant hedgerows and construct vegetated tailwater ponds. This study attempts to link habitat enhancements, biodiversity and changes in ecosystem functions by: 1. inventorying the existing biodiversity and the associated belowground community structure and composition in the various habitats of an organic farm in California’s Central Valley; and 2. monitoring key ecosystem functions of these habitats. Two years of inventories show greater native plant diversity in non-cropped areas. While nematode diversity did not differ between habitats, functional groups were clearly associated with particular habitats as were soil microbial communities (phospholipid fatty acid analysis). Earthworm diversity did not differ between habitats, but biomass was higher in non-cropped areas. Habitats with woody vegetation stored 20% of the farmscape’s total carbon (C), despite their relatively small size (only 5% of the total farm). Two years of monitoring data of farmscape C and nitrogen (N) through emissions, run-off and leaching showed distinct tradeoffs in function associated with each habitat. Clearly habitat restoration in field margins will increase both landscape biodiversity and the multifunctionality of the farmscape as a whole

Biodegradation of sorbed chemicals in soil.

Rates of biodegradation of sorbed chemicals are usually lower in soil than in aqueous systems, in part because sorption reduces the availability of the chemical to microorganisms. Biodegradation, sorption, and diffusion occur simultaneously and are tightly coupled. In soil, the rate of biodegradation is a function of a chemical's diffusion coefficient, sorption partition coefficient, the distance it must diffuse from the site of sorption to microbial populations that can degrade it, and its biodegradation rate constant. A model (DSB model) was developed that describes biodegradation of chemicals limited in the availability by sorption and diffusion. Different kinetics expressions describe biodegradation depending on whether the reaction is controlled by mass transfer (diffusion and sorption) or the intrinsic biodegradation rate, and whether biodegradation begins during or after the majority of sorption has occurred. We tested the hypothesis that there is a direct relationship between how strongly a chemical is sorbed and the chemical's biodegradation rate. In six soils with different organic carbon contents, there was no relationship between the extent or rate of biodegradation and the sorption partition coefficient for phenanthrene. Aging of phenanthrene residues in soil led to a substantial reduction in the rate of biodegradation compared to biodegradation rates of recently added phenanthrene. Considerable research has focused on identification and development of techniques for enhancing in situ biodegradation of sorbed chemicals. Development of such techniques, especially those involving inoculation with microbial strains, should consider physical mass transfer limitations and potential decreases in bioavailability over time

Spatial and seasonal variations in mercury methylation and microbial community structure in a historic mercury mining area, Yolo County, California

The relationships between soil parent lithology, nutrient concentrations, microbial biomass and community structure were evaluated in soils from a small watershed impacted by historic Hg mining. Upland and wetland soils, stream sediments and tailings were collected and analyzed for nutrients (DOC, SO4=, NO3−), Hg, MeHg, and phospholipid fatty acids (PLFA). Stream sediment was derived from serpentinite, siltstone, volcanic rocks and mineralized serpentine with cinnabar, metacinnabar and other Hg phases. Soils from different parent materials had distinct PLFA biomass and community structures that are related to nutrient concentrations and toxicity effects of trace metals including Hg. The formation of MeHg appears to be most strongly linked to soil moisture, which in turn has a correlative relationship with PLFA biomass in wetland soils. The greatest concentrations of MeHg (\u3e0.5 ng g−1MeHg) were measured in wetland soils and soil with a volcanic parent (9.5–37 µg g−1 Hg). Mercury methylation was associated with sulfate-reducing bacteria, including Desulfobacter sp. and Desulfovibrio sp., although these organisms are not exclusively responsible for Hg methylation. Statistical models of the data demonstrated that soil microbial communities varied more with soil type than with season

Soil morphology, depth and grapevine root frequency influence microbial communities in a Pinot noir vineyard

The composition of microbial communities responds to soil resource availability, and has been shown to vary with increasing depth in the soil profile. Soil microorganisms partly rely on root-derived carbon (C) for growth and activity. Roots in woody perennial systems like vineyards have a deeper vertical distribution than grasslands and annual agriculture. Thus, we hypothesized that vineyard soil microbial communities along a vertical soil profile would differ from those observed in grassland and annual agricultural systems. In a Pinot noir vineyard, soil pits were excavated to ca. 1.6–2.5m, and microbial community composition in ‘bulk’ (i.e., no roots) and ‘root’ (i.e., roots present) soil was described by phospholipid ester-linked fatty acids (PLFA). Utilization of soil taxonomy aided in understanding relationships between soil microbial communities, soil resources and other physical and chemical characteristics. Soil microbial communities in the Ap horizon were similar to each other, but greater variation in microbial communities was observed among the lower horizons. Soil resources (i.e., total PLFA, or labile C, soil C and nitrogen, and exchangeable potassium) were enriched in the surface horizons and significantly explained the distribution of soil microbial communities with depth. Soil chemical properties represented the secondary gradient explaining the differentiation between microbial communities in the B-horizons from the C-horizons. Relative abundance of Gram-positive bacteria and actinomycetes did not vary with depth, but were enriched in ‘root’ vs. ‘bulk’ soils. Fungal biomarkers increased with increasing depth in ‘root’ soils, differing from previous studies in grasslands and annual agricultural systems. This was dependent on the deep distribution of roots in the vineyard soil profile, suggesting that the distinct pattern in PLFA biomarkers may have been strongly affected by C derived from the grapevine roots. Gram-negative bacteria did not increase in concert with fungal abundance, suggesting that acidic pHs in lower soil horizons may have discouraged their growth. These results emphasize the importance of considering soil morphology and associated soil characteristics when investigating effects of depth and roots on soil microorganisms, and suggest that vineyard management practices and deep grapevine root distribution combine to cultivate a unique microbial community in these soil profiles

The interacting roles of climate, soils, and plant production on soil microbial communities at a continental scale

Soil microbial communities control critical ecosystem processes such as decomposition, nutrient cycling, and soil organic matter formation. Continental scale patterns in the composition and functioning of microbial communities are related to climatic, biotic, and edaphic factors such as temperature and precipitation, plant community composition, and soil carbon, nitrogen, and pH. Although these relationships have been well explored individually, the examination of the factors that may act directly on microbial communities vs. those that may act indirectly through other ecosystem properties has not been well developed. To further such understanding, we utilized structural equation modeling (SEM) to evaluate a set of hypotheses about the direct and indirect effects of climatic, biotic, and edaphic variables on microbial communities across the continental United States. The primary goals of this work were to test our current understanding of the interactions among climate, soils, and plants in affecting microbial community composition, and to examine whether variation in the composition of the microbial community affects potential rates of soil enzymatic activities. A model of interacting factors created through SEM shows several expected patterns. Distal factors such as climate had indirect effects on microbial communities by influencing plant productivity, soil mineralogy, and soil pH, but factors related to soil organic matter chemistry had the most direct influence on community composition. We observed that both plant productivity and soil mineral composition were important indirect influences on community composition at the continental scale, both interacting to affect organic matter content and microbial biomass and ultimately community composition. Although soil hydrolytic enzymes were related to the moisture regime and soil carbon, oxidative enzymes were also affected by community composition, reflected in the abundance of soil fungi. These results highlight that soil microbial communities can be modeled within the context of multiple interacting ecosystem properties acting both directly and indirectly on their composition and function, and this provides a rich and informative context with which to examine communities. This work also highlights that variation in climate, microbial biomass, and microbial community composition can affect maximum rates of soil enzyme activities, potentially influencing rates of decomposition and nutrient mineralization in soils

Soil-derived Nature’s Contributions to People and their contribution to the UN Sustainable Development Goals

Acknowledgments The input of PS contributes to Soils-R-GRREAT (NE/P019455/1) and the input of PS and SK contributes to the European Union's Horizon 2020 Research and Innovation Programme through project CIRCASA (grant agreement no. 774378). PR acknowledges funding from UK Greenhouse Gas Removal Programme (NE/P01982X/2). GB De Deyn acknowledges FoodShot Global for its support. TKA acknowledges the support of “Towards Integrated Nitrogen Management System (INMS) funded by the Global Environment Facility (GEF), executed through the UK’s Natural Environment Research Council (NERC). The input of DG was supported by the New Zealand Ministry of Business, Innovation and Employment (MBIE) strategic science investment fund (SSIF). PMS acknowledges support from the Australian Research Council (Project FT140100610). PM’s work on ecosystem services is supported by a National Science Foundation grant #1853759, “Understanding the Use of Ecosystem Services Concepts in Environmental Policy”. LGC is funded by National Council for Scientific and Technological Development (CNPq, Brazil – grants 421668/2018-0 and 305157/2018-3) and by Lisboa2020 FCT/EU (project 028360). BS acknowledges support from the Lancaster Environment Centre Project.Peer reviewedPostprin