Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities

Microbial traits related to ecological responses and functions could provide a common currency facilitating synthesis and prediction; however, such traits are difficult to measure directly for all taxa in environmental samples. Past efforts to estimate trait values based on phylogenetic relationships have not always distinguished between traits with high and low phylogenetic conservatism, limiting reliability, especially in poorly known environments, such as soil. Using updated reference trees and phylogenetic relationships, we estimated two phylogenetically conserved traits hypothesized to be ecologically important from DNA sequences of the 16S rRNA gene from soil bacterial and archaeal communities. We sampled these communities from an environmental change experiment in California grassland applying factorial addition of late-season precipitation and soil nutrients to multiple soil types for 3 years prior to sampling. Estimated traits were rRNA gene copy number, which contributes to how rapidly a microbe can respond to an increase in resources and may be related to its maximum growth rate, and genome size, which suggests the breadth of environmental and substrate conditions in which a microbe can thrive. Nutrient addition increased community-weighted mean estimated rRNA gene copy number and marginally increased estimated genome size, whereas precipitation addition decreased these community means for both estimated traits. The effects of both treatments on both traits were associated with soil properties, such as ammonium, available phosphorus, and pH. Estimated trait responses within several phyla were opposite to the community mean response, indicating that microbial responses, although largely consistent among soil types, were not uniform across the tree of life. Our results show that phylogenetic estimation of microbial traits can provide insight into how microbial ecological strategies interact with environmental changes. The method could easily be applied to any of the thousands of existing 16S rRNA sequence data sets and offers potential to improve our understanding of how microbial communities mediate ecosystem function responses to global changes

Evidence synthesis as the basis for decision analysis: a method of selecting the best agricultural practices for multiple ecosystem services

Agricultural management practices have impacts not only on crops and livestock, but also on soil, water, wildlife, and ecosystem services. Agricultural research provides evidence about these impacts, but it is unclear how this evidence should be used to make decisions. Two methods are widely used in decision making: evidence synthesis and decision analysis. However, a system of evidence-based decision making that integrates these two methods has not yet been established. Moreover, the standard methods of evidence synthesis have a narrow focus (e.g., the effects of one management practice), but the standard methods of decision analysis have a wide focus (e.g., the comparative effectiveness of multiple management practices). Thus, there is a mismatch between the outputs from evidence synthesis and the inputs that are needed for decision analysis. We show how evidence for a wide range of agricultural practices can be reviewed and summarized simultaneously (“subject-wide evidence synthesis”), and how this evidence can be assessed by experts and used for decision making (“multiple-criteria decision analysis”). We show how these methods could be used by The Nature Conservancy (TNC) in California to select the best management practices for multiple ecosystem services in Mediterranean-type farmland and rangeland, based on a subject-wide evidence synthesis that was published by Conservation Evidence (www.conservationevidence.com). This method of “evidence-based decision analysis” could be used at different scales, from the local scale (farmers deciding which practices to adopt) to the national or international scale (policy makers deciding which practices to support through agricultural subsidies or other payments for ecosystem services). We discuss the strengths and weaknesses of this method, and we suggest some general principles for improving evidence synthesis as the basis for multi-criteria decision analysis

A genomic catalog of Earth’s microbiomes

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes

Determinants of the introduction, naturalisation, and spread of Trifolium species in New Zealand

Two conceptual approaches which offer promise for improved understanding of biological invasions are conceptualizing the invasion process as a series of distinct stages and explicitly incorporating human actions into analyses. This study explores the utility of these approaches for understanding the invasion of Trifolium (true clover) species in New Zealand. From the published literature, I collected a range of Trifolium species attributes, including aspects of global transport and use by humans, opportunistic association with humans in New Zealand, native range attributes, habitat characteristics, and biological traits. I also searched historical records to estimate the extent to which each species had been planted in New Zealand, a search facilitated by the enormous importance of Trifolium in New Zealand's pastoral agriculture system. Regression analysis and structural equation modelling were then used to relate these variables to success at each invasion stage. Fifty-four of the 228 species in the genus Trifolium were intentionally introduced to New Zealand. Species introduced for commercial agriculture were characterised by a large number of economic uses and presence in Britain, while species introduced for horticulture or experimental agriculture were characterised by a large native range area. Nine of these 54 intentionally introduced species subsequently naturalised in New Zealand. The species that successfully naturalised were those that had been planted extensively by humans and that were well-matched to the New Zealand climate. A further 16 species (from the pool of 174 species that were never intentionally introduced) arrived and naturalised in New Zealand without any recorded intentional aid of humans. Several attributes appeared to assist species in unintentional introduction-naturalisation, including a good match to the New Zealand climate, a large native range area, presence in human-influenced habitats, a widespread distribution in Britain, and self-pollination capability. The 25 total naturalised species varied greatly in their current distributions and in the rates at which they had spread to achieve those distributions. Species that had spread quickly and are currently more widespread had been frequent contaminants in the pasture seed supply and have a long flowering period in New Zealand. Other biological traits and native range attributes played supporting roles in the spread process. Attributes facilitating success clearly varied among invasion stages. Humans played a dominant role at all stages of this invasion, although biological traits had increasing importance as a species moved through the invasion sequence. My findings suggest that incorporation of human actions and the stage-based framework provide valuable insight into the invasion process. I discuss potential avenues by which these approaches might be integrated into predictive invasion models

Nutrient and rainfall additions shift phylogenetically estimated traits of soil microbial communities

Abstract Microbial traits related to ecological responses and functions could provide a common currency facilitating synthesis and prediction; however, such traits are difficult to measure directly for all taxa in environmental samples. Past efforts to estimate trait values based on phylogenetic relationships have not always distinguished between traits with high and low phylogenetic conservatism, limiting reliability, especially in poorly known environments, such as soil. Using updated reference trees and phylogenetic relationships, we estimated two phylogenetically conserved traits hypothesized to be ecologically important from DNA sequences of the 16S rRNA gene from soil bacterial and archaeal communities. We sampled these communities from an environmental change experiment in California grassland applying factorial addition of late-season precipitation and soil nutrients to multiple soil types for 3 years prior to sampling. Estimated traits were rRNA gene copy number, which contributes to how rapidly a microbe can respond to an increase in resources and may be related to its maximum growth rate, and genome size, which suggests the breadth of environmental and substrate conditions in which a microbe can thrive. Nutrient addition increased community-weighted mean estimated rRNA gene copy number and marginally increased estimated genome size, whereas precipitation addition decreased these community means for both estimated traits. The effects of both treatments on both traits were associated with soil properties, such as ammonium, available phosphorus, and pH. Estimated trait responses within several phyla were opposite to the community mean response, indicating that microbial responses, although largely consistent among soil types, were not uniform across the tree of life. Our results show that phylogenetic estimation of microbial traits can provide insight into how microbial ecological strategies interact with environmental changes. The method could easily be applied to any of the thousands of existing 16S rRNA sequence data sets and offers potential to improve our understanding of how microbial communities mediate ecosystem function responses to global changes

Strong human association with plant invasion success for Trifolium introductions to New Zealand

It has proven difficult, when focused only on biological determinants, to explain why some plant species become naturalized in or invade new locations, whereas others fail. We analyzed the invasion of Trifolium (true clover) species into New Zealand, assessing a range of human, biogeographic, and biological influences at three key invasion stages: introduction, naturalization, and spread. We used sparse principal component analysis (SPCA) to define suites of related attributes and aggregated boosted trees to model relationships with invasion outcomes. Human and biogeographic attributes were strongly associated with success at all stages. Whereas biogeographic attributes, notably large native range, were consistently associated with success, different human factors appeared to favor success at different stages, such as presence in early trade/immigration hotspots (introduction), intentional large-scale planting (naturalization), and frequent presence as a seed contaminant (relative spread rate). Biological traits were less strongly associated with success for introduction and spread and little if at all for naturalization; we found that tall perennials with long flowering periods were more frequently selected for introduction, whereas species with extended flowering in New Zealand spread more rapidly. In addition to causal relationships, the importance of human factors may reflect indirect associations, including ecological traits associated with both human use and invasion. Nevertheless, our results highlight key roles that humans can play in facilitating plant invasion via two pathways: (i) commercial introduction leading to widespread planting and concomitant naturalization and spread and (ii) unintentional introduction and spread of species associated with human activities, such as seed contaminants

Vulnerability and resistance in the spatial heterogeneity of soil microbial communities under resource additions

Spatial heterogeneity in composition and function enables ecosystems to supply diverse services. For soil microbes and the ecosystem functions they catalyze, whether such heterogeneity can be maintained in the face of altered resource inputs is uncertain. In a 50-ha northern California grassland with a mosaic of plant communities generated by different soil types, we tested how spatial variability in microbial composition and function changed in response to nutrient and water addition. Fungal composition lost some of its spatial variability in response to nutrient addition, driven by decreases in mutualistic fungi and increases in antagonistic fungi that were strongest on the least fertile soils, where mutualists were initially most frequent and antagonists initially least frequent. Bacterial and archaeal community composition showed little change in their spatial variability with resource addition. Microbial functions related to nitrogen cycling showed increased spatial variability under nutrient, and sometimes water, additions, driven in part by accelerated nitrification on the initially more-fertile soils. Under anthropogenic changes such as eutrophication and altered rainfall, these findings illustrate the potential for significant changes in ecosystem-level spatial heterogeneity of microbial functions and communities

Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil.

Reducing tillage and growing cover crops, widely recommended practices for boosting soil health, have major impacts on soil communities. Surprisingly little is known about their impacts on soil microbial functional diversity, and especially so in irrigated Mediterranean ecosystems. In long-term experimental plots at the West Side Research and Extension Center in California's Central Valley, we characterized soil microbial communities in the presence or absence of physical disturbance due to tillage, in the presence or absence of cover crops, and at three depths: 0-5, 5-15 and 15-30 cm. This characterization included qPCR for bacterial and archaeal abundances, DNA sequencing of the 16S rRNA gene, and phylogenetic estimation of two ecologically important microbial traits (rRNA gene copy number and genome size). Total (bacterial + archaeal) diversity was higher in no-till than standard till; diversity increased with depth in no-till but decreased with depth in standard till. Total bacterial numbers were higher in cover cropped plots at all depths, while no-till treatments showed higher numbers in 0-5 cm but lower numbers at lower depths compared to standard tillage. Trait estimates suggested that different farming practices and depths favored distinctly different microbial life strategies. Tillage in the absence of cover crops shifted microbial communities towards fast growing competitors, while no-till shifted them toward slow growing stress tolerators. Across all treatment combinations, increasing depth resulted in a shift towards stress tolerators. Cover crops shifted the communities towards ruderals-organisms with wider metabolic capacities and moderate rates of growth. Overall, our results are consistent with decreasing nutrient availability with soil depth and under no-till treatments, bursts of nutrient availability and niche homogenization under standard tillage, and increases in C supply and variety provided by cover crops. Understanding how agricultural practices shift microbial abundance, diversity and life strategies, such as presented here, can assist with designing farming systems that can support high yields, while enhancing C sequestration and increasing resilience to climate change