Characterization of bacterial communities in solarized soil amended with lignocellulosic organic matter

Simmons, Christopher W.; Claypool, Joshua T.; Marshall, Megan N.; Jabusch, Lauren K.; Reddy, Amitha P.; Simmons, Blake A.; Singer, Steven W.; Stapleton, J. J.; VanderGheynst, Jean S.

doi:10.1016/j.apsoil.2013.08.014

Cited by 42 publications

(36 citation statements)

References 20 publications

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“…The gradual increases in IL concentration aided in microbial adaptation to the stressor, as advised by previous high-solids incubation studies with ionic liquids (Reddy et al 2012). Overall, increased tetra butyl and diethyl concentration caused a decline in microbial activity, as indicated by decreased respiration rates, which is consistent with prior thermophilic enrichments on switchgrass (Reddy et al 2012;Simmons et al 2014a). Identification of the exact role of each organism in green waste decomposition requires further studies.…”

Section: Discussionsupporting

confidence: 78%

“…The dominant OTU in the 75 mmol L -1 diethyl enrichment was Bacillaceae (p_Firmicutes) which is the same family that was previously found to be tolerant of 1-ethyl-3-methylimidazolium acetate on switchgrass (Reddy et al 2012;Simmons et al 2014a;Simmons et al 2014b). Here we report the dominant organism was from the family Bacillaceae but in previous studies organisms were identified down to the genus level as Bacillus coagulans (Simmons et al 2014b) and Geobacillus (Reddy et al 2012).…”

Section: Discussionmentioning

confidence: 68%

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Enrichment of microbial communities tolerant to the ionic liquids tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate

Pace

Ceballos

Harrold

et al. 2016

Appl Microbiol Biotechnol

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Aims: The aims of this study were to identify thermophilic microbial communities that degrade green waste in the presence of the ionic liquids (IL) tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate and examine preservation methods for IL tolerant communities.Methods and Results: High-solids incubations with step-wise increases in IL concentration were conducted to enrich for thermophilic IL tolerant communities. 16S rRNA sequencing of enriched communities revealed microorganisms capable of tolerating high levels of IL. Cryogenic preservation of enriched communities reduced the IL tolerance of the community and decreased the relative abundance of IL tolerant organisms. The use of cryoprotectants did not have an effect on microbial activity on green waste of the stored community. Conclusions:Step-wise increases in IL facilitated the enrichment of thermophilic, IL tolerant microbial communities that decomposed green waste. Alternative community storage and revival methods are necessary for maintenance and recovery of IL-tolerant communities.Significance and Impact of Study: A successful approach was developed to enrich communities that decompose green waste in thermophilic high-solids environments in the presence of IL. The enriched communities provide a targeted source of enzymes for the bioconversion of IL-pretreated green waste for conversion to biofuels.

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Section: Discussionsupporting

confidence: 78%

Section: Discussionmentioning

confidence: 68%

Enrichment of microbial communities tolerant to the ionic liquids tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate

Pace

Ceballos

Harrold

et al. 2016

Appl Microbiol Biotechnol

Self Cite

View full text Add to dashboard Cite

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“…Opportunistic species of nematodes and microbes quickly re-colonize after treatment and many of these groups are antagonistic to pests (Gamliel and Stapleton 1993;Mazzola et al 2012;Simmons et al 2014;Stapleton 2000), resulting in very different microbial communities than those found in either fumigated or nonfumigated soil (Drenovsky et al 2005;Shennan et al 2013). For ASD, steam and solarization, researchers continue to explore using different amendments (e.g., rice bran, brassica seed meal) to enhance pest control and optimize the carbon sources used to control specific pathogens (Fennimore et al 2014;Shennan et al 2013;Shennan et al 2014;Simmons et al 2013).…”

Section: Soil Solarization Steam and Asdmentioning

confidence: 99%

Managing for soil health can suppress pests

Hodson¹,

Lewis²

2016

Calif Agr

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A "healthy" soil can be thought of as one that functions well, both agronomically and ecologically, and one in which soil biodiversity and crop management work in synergy to suppress pests and diseases. UC researchers have pioneered many ways of managing soil biology for pest management, including strategies such as soil solarization, steam treatment and anaerobic soil disinfestation, as well as improvements on traditional methods, such as reducing tillage, amending soil with organic materials, and cover cropping. As managing for soil health becomes more of an explicit focus due to restrictions on the use of soil fumigants, integrated soil health tests will be needed that are validated for use in California. Other research needs include breeding crops for disease resistance and pest suppressive microbial communities as well as knowledge of how beneficial organisms influence plant health.

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“…During soil solarization, high temperature, limited oxygen (O 2 ) and organic enrichment alter the bacterial community structure in soil, leading to a higher dominance of thermotolerant and anaerobic species (Schönfeld et al 2003;Simmons et al 2014). The stability of an altered bacterial community structure caused by solarization in an agricultural soil in Italy was enhanced by organic enrichment with farmyard manure (Gelsomino and Cacco 2006).…”

Section: Introductionmentioning

confidence: 99%

“…Soil solarization controls a broad spectrum of pathogenic fungi, nematodes, weeds and other pests, but it also affects non-pathogenic microorganisms (Schönfeld et al 2003;Culman et al 2006;Simmons et al 2014;Yokoe et al 2015), and the nutrient release from dead microbial cells after solarization may cause a long-term increased growth response of crops (Chen et al 1991). During soil solarization, high temperature, limited oxygen (O 2 ) and organic enrichment alter the bacterial community structure in soil, leading to a higher dominance of thermotolerant and anaerobic species (Schönfeld et al 2003;Simmons et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Impact of soil solarization on the ciliate community structure of a greenhouse soil

Murase

Shinohara

Yokoe

et al. 2015

Soil Science and Plant Nutrition

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Soil solarization is an ecologically friendly method of controlling various plant pathogens and pests, but also affects non-pathogenic members of the soil biota. Here, we studied the impact of soil solarization on the community structure of soil ciliates using a culture-independent molecular approach, namely denaturing gradient gel electrophoresis (DGGE) of targeted 18S rRNA gene fragments. Greenhouse soil with added organic fertilizers was solarized for 33 days at an average temperature of 47-48°C. Solarization caused a drastic change in the ciliate community. The variation between replicates was large, which suggested that the distribution of ciliates was spatially heterogeneous in the soil, probably due to their decreased numbers. In contrast, non-solarized soil had a stable and homogeneous ciliate community during the experimental period. In solarized soil, most of the original ciliate community recovered 76 days after solarization. Sequence analysis of DGGE fragments indicated that both r-selected and K-selected species of ciliates were affected by solarization but recovered with time after solarization. Our results demonstrated both the vulnerability and resilience of the ciliate community to soil solarization and also the utility of using molecular-based analysis of ciliate communities as bioindicators of soil stress caused by solarization.

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Characterization of bacterial communities in solarized soil amended with lignocellulosic organic matter

Cited by 42 publications

References 20 publications

Enrichment of microbial communities tolerant to the ionic liquids tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate

Enrichment of microbial communities tolerant to the ionic liquids tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate

Managing for soil health can suppress pests

Impact of soil solarization on the ciliate community structure of a greenhouse soil

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