To account for sequence read depth variation per sample, the fungal OTU table was normalized by rarefying to equal fungal sequence reads , using the ‘rarefy’ command in VEGAN in R to account for uneven sequencing depth across samples.Our study demonstrates that greater crop diversity in intensive agricultural systems drives a richer and more diverse AMF community. We observed nearly twice as many AMF taxa in poly cultures than in mono cultures, while accounting for variation in soil properties that also significantly affected AMF richness. The AMF community composition in poly culture sites was also distinct from that in monoculture field sites, but soil properties played a stronger role in structuring the AMF community. Contrary to our expectations, we also show that AMF colonization of roots is probably driven by plant host identity rather than farm management practices . For both AMF diversity and colonization responses, soil properties were important factors that influenced the outcomes, but did not dominate relative to the important effect of higher crop diversity. Overall our findings indicate that managing for crop diversity in agricultural landscapes can strongly influence AMF community composition, including richness and diversity, across heterogeneous soils. Further, our results support the notion that plant diversity is key to below ground biodiversity, which in turn could support multifunctional agroecosystems , including those that have been intensively managed in the past. We show that poly culture fields harbor a richer and more diverse AMF community than do monoculture fields, suggesting that poly culture plantings may promote recovery of AMF richness following a long period of monoculture farming, which is known to be associated with decreased AMF diversity . Our poly culture sites were formerly farmed intensively as mono cultures, as recently as 7 yr before sampling, and thus were likely to have had a depauperate AMF community.How to build a vertical hydroponic system? Soil properties also contributed to explaining some of the variance in AMF richness and diversity, but overall they played a minimal role. While AMF are ubiquitous across landscapes, AMF are obligate symbionts with a degree of host specificity; thus, AMF associations with plant hosts are typically not random . Variation in plant traits, including phenology, root architecture and other factors, impacts the distribution and composition of AMF,and thus functionally different plants can associate with distinct AMF communities.

In our study, we found evidence that different AMF taxa occur in poly cultures vs mono cultures. A Rhizophagus taxon was the top indicator of mono cultures, whereas the top indicator taxon in poly cultures was in the genus Glomus. While research on AMF functional traits is still emerging , these taxonomic differences , coupled with greater AMF diversity in poly cultures, could indicate differences in AMF community functionality with implications for plant performance and ecosystem processes. Future research should focus on these possible functional differences among AMF taxa. In poly cultures, functionally distinct plant hosts are planted across space and time, creating a mosaic of diverse microhabitats, varying in microclimatic and microedaphic properties, as evidenced by our finding that poly cultures have a more heterogenous soil environment compared with mono cultures. Across poly culture fields in our study system, crop type can be distinct row by row in space, but single rows can also shift from crop to crop at different times throughout the year. For example, annuals and perennial crops are grown together at the same time, grasses and tubers can be grown adjacent to each other, and leafy greens and legumes could be grown sequentially in poly culture fields in this study system. In fact, the presence of perennials and legumes has been shown to increase AMF diversity. In the poly culture field sites, not only are legumes present, but functionally distinct leguminous species and cultivars are planted . Therefore, the likely mechanism that fosters a richer and more diverse AMF community in poly cultures is the heterogeneity in plant composition: over space, across time within a space, and as different species or varieties across and within functional types such as legumes. Arbuscular mycorrhizal fungi communities also depend, in part, on the composition and pattern of past plant communities . This may explain why in poly cultures we do not find a more diverse AMF community in the more plant-rich transects when compared with the single species transects. Instead, the legacy of poly culture management, specifically the temporally, spatially and functionally heterogeneous plant community, leads to an overall richer and more diverse AMF community in poly cultures than in mono cultures. Poly cultures also harbored a distinct AMF community from mono cultures. However, AMF communities were quite heterogeneous across both monoculture and poly culture field sites, reflecting a high turnover among sites. The heterogeneity and high turnover of the AMF community are evident in the fact that average site-level AMF richness is much lower than total AMF richness recorded across all sites: the average AMF richness was c. 5 in monoculture and 10 in poly culture field sites, compared with a total AMF richness in the whole study of 244. Arbuscular mycorrhizal fungi communities tend to be heterogeneous even at fine scales.

Our expectation that AMF communities on poly culture farms would be more heterogeneous at a fine scale than those on mono cultures was not borne out; specifically, we found no interaction between farm management and transect for composition. This is further evidence that poly cultures may impart a legacy effect on AMF communities. Despite possible AMF compositional differences between mono cultures and poly cultures, our results show that soil properties played a larger role in explaining AMF community composition than farm management, with pH being a significant predictor, consistent with other studies , especially at finer spatial scales . The greater heterogeneity in soil edaphic properties in poly cultures than mono cultures suggests that crop diversity may indirectly underlie these edaphic-driven patterns of AMF community structure. Regardless, these findings suggest a role for soil properties in structuring AMF community composition across farms and a role for farm management in shifting the available AMF community into more or less diverse communities at the site level. The role of plant diversity vs plant host identity on AMF associations was most evident in our measurements of AMF colonization in roots. Our study design allowed us to explore whether crop diversity impacted AMF colonization in the same crop species, and also whether different crop plant hosts in poly cultures play a role in determining AMF colonization. Contrary to our expectation, we found no difference in AMF colonization across the same crop host when planted in poly culture or monoculture fields. In part, this may be explained by fertilizer usage across all farms, which may mask or suppress changes in AMF root colonization as a result of increasing crop diversity because fertilization decreases the dependency of plants hosts on AMF . But AMF colonization has been shown to increase in plant host roots within more diverse plant communities , especially when highly mycorrhizal plants are present . Instead, we found similar degrees of AMF colonization on the focal crop host between poly culture and monoculture farms, but greater degrees of AMF colonization on other crop hosts on poly culture fields. Recent research has found mixed results about the extent to which plant host identity determines the quantity of AMF colonization. Some studies show that plant identity rarely plays a role , while others, like this study, demonstrate that plant host identity does impact AMF colonization, especially at local scales.

Thus, our study strengthens the body of research showing that AMF colonization is dependent on specific AMF–plant host associations. While this finding could suggest that agricultural systems with higher plant diversity may not benefit from greater AMF colonization, AMF colonization may not actually be the most important indicator of AMF benefits and functions for crops in agricultural systems . Colonization does not indicate the extent of nutrient transfer or the degree of ecosystem services provided by AMF . Instead,vertical plant growing there is a growing understanding that AMF composition is an important determinant of the benefits received by ecosystems from AMF communities . A richer and more diverse AMF community could indicate differences in ecosystem functioning between monoculture and poly culture farming, with important implications for agricultural management. Previous research has shown that mono cultures contribute to reducing AMF richness and can change community composition to favor less beneficial AMF taxa, in turn contributing to yield declines . Although empirical evidence from field studies on AMF remains rare, a positive relationship between AMF diversity and ecosystem functioning is expected because AMF taxa differ in their functions . For example, studies have shown differential plant productivity responses to different AMF taxa or communities . Other studies have demonstrated that productivity, phosphorus uptake, soil aggregation and pathogen protection increase with AMF diversity . In short, as AMF taxa are functionally heterogenous,a more diverse community could provide a wider array and/or stability of functions.Therefore, crops grown in poly cultures may benefit from the enhanced and/or stabilized ecosystem functions and services of a richer and more diverse AMF community.As pressures from habitat loss increase, there is growing interest in agricultural landscapes as potential habitat or movement areas for wildlife. Agricultural landscapes are potentially rich in structure, food, and cover, and many native species forage and reproduce in these landscapes. These lands can support moderate diversity of birds, mammals, arthropods, and plants, depending on the intensity of agriculture and on configuration of natural land cover. Mammalian carnivores are frequent targets of conservation efforts, and they play a key role in food webs, for example via mesopredator release or trophic downgrading. Because carnivores are typically wide-ranging, it is especially important to consider agricultural landscapes as well as protected areas when forming conservation plans for these species. Wildlife managers and conservation planners currently have little knowledge of carnivore use of agricultural landscapes, but this subject will become increasingly important as agricultural systems continue to expand and protected areas become more isolated. Connectivity between habitat patches is especially critical in human-dominated landscapes, but most connectivity models focus on natural vegetation types, not on differences between human-dominated land cover types within such landscapes. When evaluating landscape connectivity for large carnivores, conservation planners have often relied on expert opinion and considered all agriculture as having uniformly low connectivity value . Many members of the order Carnivora are omnivorous and feed, in part, on anthropogenic food sources. Scat analysis has identified cultivated fruit in the diets of carnivores, particularly foxes and stone martens, and Borchert et al.found that at least one orchard type – avocado – was regularly used by carnivores in California. California is a major producer of avocados, with 23,500 hectares of orchards spread across five southern counties. Because avocados grow well on steep slopes, they are planted in a variety of landscape contexts, including hill slopes adjacent to native vegetation as well as valley bottoms adjacent to other types of crops. We examined the use of avocado orchards by mammalian carnivores across agricultural-wild land gradients in southern California. We assessed whether occupancy of carnivores at motion-activated camera stations was a function of surrounding land cover, and in particular, whether area of orchards influenced carnivore occupancy. If orchards constitute poor quality carnivore habitat relative to natural areas, we would expect to observe carnivores less frequently in orchards than in nearby wild lands.Coastal southern California is highly urbanized and contains about two thirds of California’s 38 million residents; it also has relatively little remaining undeveloped land, yet is experiencing rapid population growth. This region has a Mediterranean-type climate, and the dominant natural vegetation types areoak woodland, riparian woodland, sage scrub, and annual grassland. Eleven native members of the order Carnivora occur in this region: American badger , American black bear , bobcat , coyote , gray fox , long-tailed weasel , mountain lion , raccoon , ring tail , striped skunk , and Western spotted skunk . Our study area included avocado orchards and wild lands in Santa Barbara and Ventura counties selected for their position in the landscape and for landowner cooperation .