Factors affecting soil microbial community structure in tomato cropping systems
Introduction
The microbial community composition of agricultural soils is influenced by a wide variety of factors. Physical, chemical, and biological factors that are believed to affect microbial community composition include soil type and texture (Buyer et al., 1999, Buyer et al., 2002, Cavigelli et al., 2005, Gelsomino et al., 1999, Girvan et al., 2003, Ulrich and Becker, 2006), aggregate size (Schutter and Dick, 2002), moisture (Buckley and Schmidt, 2001b, Griffiths et al., 2003, Williams and Rice, 2007), predation (Griffiths et al., 1999), pH (Fierer and Jackson, 2006), and temperature (Norris et al., 2002). Agricultural management factors include tillage (Buckley and Schmidt, 2001a, Cookson et al., 2008), cover cropping (Carrera et al., 2007, Schutter et al., 2001), fertilizer (Grayston et al., 2004), organic amendments (Saison et al., 2006), and crop rotation (Olsson and Alström, 2000). Many of these factors interact with each other and have both direct and indirect effects on the soil microbial community. For example, a winter cover crop would add organic carbon to the soil through rhizodeposition, and if the crop residue was mowed and left in place it would both reduce water evaporation and suppress weeds. In this example one management factor has at least three potential mechanisms for affecting the soil ecosystem.
This complexity of interacting factors makes it difficult to parse the dominant drivers of microbial community structure into explicitly measurable variables. In many cases, studies are limited due to an inability to control many of the factors influencing the microbial community and evaluation must rely on alternative metagenomic approaches which can be cost prohibitive (Shi et al., 2009). Agroecosystems, on the other hand, offer environmental sites that generally have well defined histories and often have well controlled factors that have been shown to influence soil community dynamics (Minoshima et al., 2007, Wang et al., 2007a). Additionally, determination of factors that influence microbial community composition in the field will have significant impact on understanding how management practices affect crop quality (Barrett et al., 2007), disease ecology (Zhou and Everts, 2007), and biogeochemical cycling (Hawkes et al., 2005, Mills et al., 1999). The agroecosystems described in this paper included several gradients across many of the variables that influence microbial populations and offered an opportunity to test hypotheses regarding the relative importance of these factors.
Tomatoes and other high-value crops are often grown on raised beds covered with black polyethylene (Hochmuth et al., 2008). The black polyethylene raises early season soil temperature, suppresses weeds, and conserves soil moisture. When combined with drip irrigation, synthetic fertilizers, and pesticides, this cropping system can produce high yields of marketable produce. However, use of this system can result in degradation of soil quality, increased runoff of contaminated water, and raised production costs (Rice et al., 2001). Alternative systems that use renewable resources and minimize soil tillage have been developed to improve environmental quality while maintaining profitability (Abdul-Baki and Teasdale, 1997, Rice et al., 2001).
In a tomato production system developed at the Beltsville Agricultural Research Center (Abdul-Baki and Teasdale, 1997), raised beds are formed each fall and seeded with hairy vetch. In the spring the vetch is mowed and the tomato seedlings are planted through the vetch residue without tilling. The vetch provides nitrogen and organic carbon to the soil and suppresses weeds. The surface layer of decomposing vetch shoots also reduces surface runoff and prevents splashing of soil onto the lower tomato leaves and fruit. While tomatoes grown under black plastic produce an earlier crop, tomatoes grown under vetch produce for a longer period of time and are less susceptible to disease (Kumar et al., 2004).
In a previous study on tomato cropping systems (Carrera et al., 2007) we found that cover cropping with hairy vetch had a greater impact on soil microbial communities than amending with compost or manure. We were unable to determine whether the differences in microbial communities between cover-cropped and black polyethylene-covered soils were due to nutrient inputs from the cover crops, soil temperature increases from the black polyethylene, both of these, or other unexplored factors. In this paper we use phospholipid fatty acid (PLFA) analysis to test the following hypotheses:
- (1)
Temperature and moisture differences between polyethylene-covered and cover-cropped treatments are partly responsible for treatment effects on soil microbial community composition, and
- (2)
Different species of cover crops have unique root and shoot effects on soil microbial community composition.
Section snippets
Field experiment
This experiment was conducted at the USDA-ARS Beltsville Agricultural Research Center, Beltsville, Maryland, in the same field in 2005 and 2007 and in an adjacent field in 2006. Soils were mixed Hapludults and Endoaquults in the order Ultisols. Soils were classified according to the USDA texture classification scheme as sandy loam or loamy sand, varying between 63 and 83 percent sand, 7–27 percent silt, and 2–16 percent clay.
In the September before the tomato cropping season, lime and nutrients
Cover crop biomass and tomato yield
Rye and hairy vetch cover crops established well and produced abundant biomass by the time of mowing in all years. Rye and hairy vetch above-ground biomass averaged 5940 and 6230 kg ha−1, respectively, whereas rye and hairy vetch root biomass averaged 2150 and 460 kg ha−1, respectively. The lower root than shoot biomass values, particularly those for hairy vetch roots, are consistent with findings of other researchers (Sainju et al., 2005).
There were few differences in marketable yield among
Discussion
In this study our goal was to identify and prioritize some of the factors that contributed to soil and rhizosphere microbial biomass and community composition in a tomato production agroecosystem. This task is difficult due to interactions, correlations, and shared variance between treatments and environmental variables. Despite these complexities we were able to assign significant proportions of shared variance to particular mechanisms by which cover cropping and plasticulture affect soil and
Acknowledgements
We thank Stanley Tesch, Ruth Mangum, Peter Ewashkow, Laurie McKenna, and Steve Rogers for technical assistance. We thank Christopher Blackwood and Matt Kramer for statistical advice.
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Current address: USDA, ARS, Horticultural Crops Research Laboratory, Corvallis, OR, USA.