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.

Fungi are important members of soil microbial communities in row-crop and grassland soils, provide essential ecosystem services such as nutrient cycling, organic matter decomposition, and soil structure, but fungi are also more sensitive to physical disturbance than other microorganisms. Adoption of conservation management practices such as no-till and cover cropping shape the structure and function of soil fungal communities. No-till eliminates or greatly reduces the physical disturbance that redistributes organisms and nutrients in the soil profile and disrupts fungal hyphal networks, while cover crops provide additional types and greater abundance of organic carbon sources. In a long-term, row crop field experiment in California's Central Valley we hypothesized that a more diverse and plant symbiont-enriched fungal soil community would develop in soil managed with reduced tillage practices and/or cover crops compared to standard tillage and no cover crops. We measured the interacting effects of tillage and cover cropping on fungal communities based on fungal ITS sequence assigned to ecological guilds. Functional groups within fungal communities were most sensitive to longterm tillage practices, with 45% of guild-assigned taxa responding to tillage, and a higher proportion of symbiotroph taxa under no-till. In contrast, diversity measures reflected greater sensitivity to cover crops, with higher phylogenetic diversity observed in soils managed with cover crops, though only 10% of guild-assigned taxa responded to cover crops. The relative abundance of pathotrophs did not vary across the management treatments. Cover cropping increased species diversity, while no-till shifted the symbiotroph:saprotroph ratio to favor symbiotrophs. These management-induced shifts in fungal community composition could lead to greater ecosystem resilience and provide greater access of crops to limiting resources.

4The impact on soil health of long-term no-tillage (NT) and cover cropping (CC) practices, alone 5 and in combination, was measured and compared with standard tillage (ST) with and without 6 cover crops (NO) in irrigated row crops after 15 years of management in the San Joaquin Valley 7 (SJV) CA, USA. Soil aggregation, rates of water infiltration, content of carbon, nitrogen, water 8 extractable organic carbon (WEOC) and organic nitrogen (WEON), residue cover, and 9 biological activity were all increased by NT and CC practices relative to STNO. However, 10 effects varied by depth with NT increasing soil bulk density by 12% in the 0 -15 cm depth and 11 10% in the 15 -30 cm depth. Higher levels of WEOC were found in the CC surface (0 -5cm) 12 depth in both spring and fall samplings in 2014. Surface layer (0 -15 cm) WEON was higher in 13 the CC systems for both samplings. Tillage did not affect WEON in the spring, but WEON was 14 increased in the NT surface soil layer in the fall. Sampling depth, CC, and tillage affected 1-15 day soil respiration and a soil health index assessment, however the effects were seasonal, with 16 higher levels found in the fall sampling than in the spring. Both respiration and the soil health 17 index were increased by CC with higher levels found in the 0 -5 cm depth than in the 5 -15 and 18 15 -30 cm depths. Results indicated that adoption of NT and CC in arid, irrigated cropping 19 systems could benefit soil health by improving chemical, physical, and biological indicators of 20 soil functions while maintaining similar crop yields as the ST system. 21 . 22 23 Keywords 24

A hallmark characteristic of species of Aeromonas is their ability to secrete a wide variety of enzymes associated with pathogenicity and environmental adaptability. Among the most intensively studied are beta-lactamases, lipases, hemolytic enterotoxins, proteases, chitinases, nucleases and amylases. Multiple copies of genes encoding each type of enzyme provide additional biological diversity. Except for the chitinases, these multiple copies show little evolutionary relatedness at the DNA level and only limited similarity at the protein level. Indeed a number of the genes, such as nuclease H of A. hydrophila, have no similarity to known prokaryotic or eukaryotic sequences. The challenge is to determine how these genes evolved, where they originated and why Aeromonas possesses them in such abundance and variety.

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