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.

Soil and soil biodiversity play critical roles in Nature's Contributions to People (NCP) # 10, defined as Nature's ability to regulate direct detrimental effects on humans, and on human-important plants and animals, through the control or regulation of particular organisms considered to be harmful. We provide an overview of pathogens in soil, focusing on human and crop pathogens, and discuss general strategies, and examples, of how soils' extraordinarily diverse microbial communities regulate soil-borne pathogens. We review the ecological principles underpinning the regulation of soil pathogens, as well as relationships between pathogen suppression and soil health. Mechanisms and specific examples are presented of how soil and soil biota are involved in regulating pathogens of humans and plants. We evaluate how specific agricultural management practices can either promote or interfere with soil's ability to regulate pathogens. Finally, we conclude with how integrating soil, plant, animal and human health through a ‘One Health’ framework could lead to more integrated, efficient and multifunctional strategies for regulating detrimental organisms and processes. This article is part of the theme issue ‘The role of soils in delivering Nature's Contributions to People’.

Methylibium petroleiphilum PM1 is a well-characterized environmental strain capable of complete metabolism of the fuel oxygenate methyl tert -butyl ether (MTBE). Using a molecular genetic system which we established to study MTBE metabolism by PM1, we demonstrated that the enzyme MdpA is involved in MTBE removal, based on insertional inactivation and complementation studies. MdpA is constitutively expressed at low levels but is strongly induced by MTBE. MdpA is also involved in the regulation of tert -butyl alcohol (TBA) removal under certain conditions but is not directly responsible for TBA degradation. Phylogenetic comparison of MdpA to related enzymes indicates close homology to the short-chain hydrolyzing alkane hydroxylases (AH1), a group that appears to be a distinct subfamily of the AHs. The unique, substrate-size-determining residue Thr ⁵⁹ distinguishes MdpA from the AH1 subfamily as well as from AlkB enzymes linked to MTBE degradation in Mycobacterium austroafricanum .

California has unsustainable use of agricultural water and energy, as well as problems of severe drought, nitrate pollution and groundwater salinity. As the leading producer and exporter of agricultural produce in the United States, 5.6 percent of California’s energy is currently used for pumping groundwater. These problems and new regulatory policies (e.g., Sustainable Groundwater Management Act, Irrigated Lands Regulatory Program) pressure growers to schedule, account and maintain records of water, energy and nutrients needed for crop and soil management. Growers require varying levels of decision support to integrate different irrigation strategies into farm operations. Decision support can come from the public or private sector, where there are many tradeoffs between cost, underlying science, user friendliness and overall challenges in farm integration. Thus, effective irrigation management requires clear definitions, decision support and guidelines for how to incorporate and evaluate the water–nutrient–energy nexus benefits of different practices and combinations of practices under shifting water governance. The California Energy Commission-sponsored Energy Product Evaluation Hub (Cal-EPE Hub) project has a mission of providing science-based evaluation of energy-saving technologies as a direct result of improved water management for irrigation in agriculture, including current and future irrigation decision support systems in California. This project incorporates end-user perceptions into evaluations of existing decision support tools in partnership with government, agricultural and private stakeholders. In this article, we review the policy context and science underlying the available irrigation decision support systems (IDSS), discuss the benefits/tradeoffs and report on their efficacy and ease of use for the most prevalent cropping systems in California. Finally, we identify research and knowledge-to-action gaps for incorporating irrigation decision support systems into new incentives and requirements for reporting water and energy consumption as well as salinity and nitrogen management in the state of California.