Factors affecting soil microbial community structure in tomato cropping systems

https://doi.org/10.1016/j.soilbio.2010.01.020Get rights and content

Abstract

Soil and rhizosphere microbial communities in agroecosystems may be affected by soil, climate, plant species, and management. The management and environmental factors controlling microbial biomass and community structure were identified in a three-year field experiment. The experiment consisted of a tomato production agroecosystem with the following nine treatments: bare soil, black polyethylene mulch, white polyethylene mulch, vetch cover crop, vetch roots only, vetch shoots only, rye cover crop, rye roots only, and rye shoots only. The following hypotheses were tested: (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. Microbial biomass and community composition were measured by phospholipid fatty acid analysis. Microbial biomass was increased by all cover crop treatments, including root only and shoot only. Cover cropping increased the absolute amount of all microbial groups, but Gram-positive bacteria decreased in proportion under cover crops. We attribute this decrease to increased readily available carbon under cover-cropped treatments, which favored other groups over Gram-positive bacteria. Higher soil temperatures under certain treatments also increased the proportion of Gram-positive bacteria. Vetch shoots increased the amount and proportion of Gram-negative bacteria, fungi, and arbuscular mycorrhizal fungi in the rhizosphere of tomato plants. The imposed treatments were much more significant than soil temperature, moisture, pH, and texture in controlling microbial biomass and community structure.

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.

References (65)

  • P.A. Olsson

    Signature fatty acids provide tools for determination of the distribution and interactions of mycorrhizal fungi in soil

    FEMS Microbiology Ecology

    (1999)
  • S. Olsson et al.

    Characterisation of bacteria in soils under barley monoculture and crop rotation

    Soil Biology and Biochemistry

    (2000)
  • O. Ouariti et al.

    Cadmium- and copper-induced changes in tomato membrane lipids

    Phytochemistry

    (1997)
  • A.D. Peacock et al.

    Soil microbial community responses to dairy manure or ammonium nitrate applications

    Soil Biology and Biochemistry

    (2001)
  • A.W. Ratcliff et al.

    Changes in microbial community structure following herbicide (glyphosate) additions to forest soils

    Applied Soil Ecology

    (2006)
  • A.D. van Diepeningen et al.

    Effects of organic versus conventional management on chemical and biological parameters in agricultural soils

    Applied Soil Ecology

    (2006)
  • M.A. Williams

    Response of microbial communities to water stress in irrigated and drought-prone tallgrass prairie soils

    Soil Biology and Biochemistry

    (2007)
  • M.A. Williams et al.

    Carbon flow from 13C-labeled straw and root residues into the phospholipid fatty acids of a soil microbial community under field conditions

    Soil Biology and Biochemistry

    (2006)
  • M.A. Williams et al.

    Seven years of enhanced water availability influences the physiological, structural, and functional attributes of a soil microbial community

    Applied Soil Ecology

    (2007)
  • L. Zelles

    Phospholipid fatty acid profiles in selected members of soil microbial communities

    Chemosphere

    (1997)
  • L. Zelles et al.

    Changes in soil microbial properties and phospholipid fatty acid fractions after chloroform fumigation

    Soil Biology and Biochemistry

    (1997)
  • A. Abdul-Baki et al.

    Sustainable Production of Fresh-Market Tomatoes and Other Vegetables with Cover Crop Mulches

    (1997)
  • A.A. Abdul-Baki et al.

    Nitrogen requirements of fresh-market tomatoes on hairy vetch and black polyethylene mulch

    HortScience

    (1997)
  • D.M. Barrett et al.

    Qualitative and nutritional differences in processing tomatoes grown under commercial organic and conventional production systems

    Journal of Food Science

    (2007)
  • D.A. Bossio et al.

    Impacts of carbon and flooding on soil microbial communities: phospholipid fatty acid profiles and substrate utilization patterns

    Microbial Ecology

    (1998)
  • D.A. Bossio et al.

    Determinants of soil microbial communities: effects of agricultural management, season, and soil type on phospholipid fatty acid profiles

    Microbial Ecology

    (1998)
  • D. Buckley et al.

    The structure of microbial communities in soil and the lasting impact of cultivation

    Microbial Ecology

    (2001)
  • J.S. Buyer et al.

    Microbial community structure and function in the spermosphere as affected by soil and seed type

    Canadian Journal of Microbiology

    (1999)
  • J.S. Buyer et al.

    Soil and plant effects on microbial community structure

    Canadian Journal of Microbiology

    (2002)
  • J.W. Doran et al.

    Influence of alternative and conventional agricultural management on soil microbial processes and nitrogen availability

    American Journal of Alternative Agriculture

    (1987)
  • R.E. Drenovsky et al.

    Soil water content and organic carbon availability are major determinants of soil microbial community composition

    Microbial Ecology

    (2004)
  • S. el Fantroussi et al.

    Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles

    Applied and Environmental Microbiology

    (1999)
  • Cited by (249)

    View all citing articles on Scopus
    1

    Current address: USDA, ARS, Horticultural Crops Research Laboratory, Corvallis, OR, USA.

    View full text