Soil microbial biomass and enzyme data after six years of cover crop and compost treatments in organic vegetable production.

Cover crops and compost are organic matter inputs that can impact soil health in tillage-intensive, high-input, organic vegetable production systems in the central coast region of California. Data are presented on soil microbial biomass (carbon and nitrogen) and soil enzymes (ß-glucosidase, ß-glucosaminidase, alkaline phosphatase, aspartase and L-asparaginase and dehydrogenase) from a relatively long-term organic systems experiment in Salinas, California that was focused on lettuce and broccoli production and included eight different certified organic systems. These systems differed in compost inputs, cover cropping frequency, cover crop type, and cover cropping seeding rate. The compost was made from urban yard waste, and the cover crops included rye, a legume-rye mixture, and a mustard mixture planted at two seeding rates (standard rate 1× versus high rate 3×). There were three legume-rye 3× systems that differed in compost inputs (0 versus 15 Mg ha-1 year-1 and cover cropping frequency (every winter versus every fourth winter). The data in this article support and augment information presented in the research articles "Cover cropping frequency is the main driver of soil microbial changes during six years of organic vegetable production" (Brennan and Acosta-Martinez, 2017) and "Cover crops and compost influence soil enzymes during 6 years of tillage-intensive, organic vegetable production" (Brennan and Acosta-Martinez, 2018).

Efficient Identification of Causal Mutations through Sequencing of Bulked F 2 from Two Allelic Bloomless Mutants of Sorghum bicolor.

Sorghum (Sorghum bicolor Moench, L.) plant accumulates copious layers of epi-cuticular wax (EW) on its aerial surfaces, to a greater extent than most other crops. EW provides a vapor barrier that reduces water loss, and is therefore considered to be a major determinant of sorghum's drought tolerance. However, little is known about the genes responsible for wax accumulation in sorghum. We isolated two allelic mutants, bloomless40-1 (bm40-1) and bm40-2, from a mutant library constructed from ethyl methane sulfonate (EMS) treated seeds of an inbred, BTx623. Both mutants were nearly devoid of the EW layer. Each bm mutant was crossed to the un-mutated BTx623 to generated F2 populations that segregated for the bm phenotype. Genomic DNA from 20 bm F2 plants from each population was bulked for whole genome sequencing. A single gene, Sobic.001G228100, encoding a GDSL-like lipase/acylhydrolase, had unique homozygous mutations in each bulked F2 population. Mutant bm40-1 harbored a missense mutation in the gene, whereas bm40-2 had a splice donor site mutation. Our findings thus provide strong evidence that mutation in this GDSL-like lipase gene causes the bm phenotype, and further demonstrate that this approach of sequencing two independent allelic mutant populations is an efficient method for identifying causal mutations. Combined with allelic mutants, MutMap provides powerful method to identify all causal genes for the large collection of bm mutants in sorghum, which will provide insight into how sorghum plants accumulate such abundant EW on their aerial surface. This knowledge may facilitate the development of tools for engineering drought-tolerant crops with reduced water loss.

The influence of multiwalled carbon nanotubes on polycyclic aromatic hydrocarbon (PAH) bioavailability and toxicity to soil microbial communities in alfalfa rhizosphere.

Carbon nanotubes (CNTs) may affect bioavailability and toxicity of organic contaminants due to their adsorption properties. Recent studies have observed the influence of multiwalled carbon nanotubes (MWNTs) on the fate of polycyclic aromatic hydrocarbons (PAHs) and other organic contaminants. Greenhouse studies (49 d) were conducted with alfalfa plants in two different soil types. Four treatment conditions (0, 25, 50, or 100 mg/kg MWNTs+100 mg/kg PAHs mixture-pyrene and phenanthrene) were tested in order to determine their effects on soil microbial community composition and PAH residues. Microbial community structure in the two highest treatments (50 mg/kg and 100 mg/kg MWNTs) showed a dramatic shift in the presence of MWNTs in sandy loam soil (1% organic matter) in comparison to the control (0 mg/kg MWNTs). Many microbial fatty acid methyl ester (FAMEs) markers (i15:0, 16:1ω5c, 10Me17:0, 10Me16:0) were missing in the control soil. However, there was a lower abundance of these FAMEs in the 25 mg/kg MWNT treatment (except 10Me17:0) and a higher presence of these FAMEs in the 50 mg/kg and 100 mg/kg MWNT treatments compared to control. In contrast, microbial community composition was not influenced by the MWNT treatments in sandy clay loam soil (5.9% organic matter). However, pyrene degradation in sandy clay loam soil significantly increased by 21% in the highest MWNT treatment group (100 mg/kg) and 9.34% in 50 mg/kg MWNT treatment. Under the conditions tested in this study, MWNTs significantly impacted the soil microbial community distribution and PAH degradation and effects were dependent on soil types, specifically organic matter content.

Soil microbial and nutrient responses to 7 years of seasonally altered precipitation in a Chihuahuan Desert grassland.

Soil microbial communities in Chihuahuan Desert grasslands generally experience highly variable spatiotemporal rainfall patterns. Changes in precipitation regimes can affect belowground ecosystem processes such as decomposition and nutrient cycling by altering soil microbial community structure and function. The objective of this study was to determine if increased seasonal precipitation frequency and magnitude over a 7-year period would generate a persistent shift in microbial community characteristics and soil nutrient availability. We supplemented natural rainfall with large events (one/winter and three/summer) to simulate increased precipitation based on climate model predictions for this region. We observed a 2-year delay in microbial responses to supplemental precipitation treatments. In years 3-5, higher microbial biomass, arbuscular mycorrhizae abundance, and soil enzyme C and P acquisition activities were observed in the supplemental water plots even during extended drought periods. In years 5-7, available soil P was consistently lower in the watered plots compared to control plots. Shifts in soil P corresponded to higher fungal abundances, microbial C utilization activity, and soil pH. This study demonstrated that 25% shifts in seasonal rainfall can significantly influence soil microbial and nutrient properties, which in turn may have long-term effects on nutrient cycling and plant P uptake in this desert grassland.

An evaluation of the impact of multiwalled carbon nanotubes on soil microbial community structure and functioning.

This study evaluated the impacts of multiwalled carbon nanotubes (MWNTs) on microbial community composition and functioning in a sandy loam soil over 90 d. We used test concentrations in the range of lower MWNT concentrations (10mg/kg) to extremely high MWNT concentrations (10,000 mg/kg) as a worst case scenario. We observed no effects of MWNTs on soil respiration, enzymatic activities, and microbial community composition at 10, 100 and 1,000 mg/kg. However, increases in fungal fatty acid methyl ester markers were observed at the highest treatment. In addition, pyrosequencing demonstrated a decreased abundance of some bacterial genera like Derxia, Holophaga, Opitutus and Waddlia at the highest treatment while bacterial genera that are considered potential degraders of recalcitrant contaminants (such as polycyclic aromatic hydrocarbons) like Rhodococcus, Cellulomonas, Nocardioides and Pseudomonas increased. These results suggest a shift in soil microbial community composition to more tolerant microbial populations in the presence of extremely high MWNT concentrations. It is unlikely that the change observed at 10,000 mg/kg is due to metal or carbon impurities as the MWNTs used in this study were of high purity. Given the need for wide-ranging data for regulation and risk assessment of nanomaterials, this study provides valuable data.

Pyrosequencing reveals bacteria carried in different wind-eroded sediments.

Little is known about the microbial communities carried in wind-eroded sediments from various soil types and land management systems. The novel technique of pyrosequencing promises to expand our understanding of the microbial diversity of soils and eroded sediments because it can sequence 10 to 100 times more DNA fragments than previous techniques, providing enhanced exploration into what microbes are being lost from soil due to wind erosion. Our study evaluated the bacterial diversity of two types of wind-eroded sediments collected from three different organic-rich soils in Michigan using a portable field wind tunnel. The wind-eroded sediments evaluated were a coarse sized fraction with 66% of particles >106 µm (coarse eroded sediment) and a finer eroded sediment with 72% of particles <106 µm. Our findings suggested that (i) bacteria carried in the coarser sediment and fine dust were effective fingerprints of the source soil, although their distribution may vary depending on the soil characteristics because certain bacteria may be more protected in soil surfaces than others; (ii) coarser wind-eroded sediment showed higher bacterial diversity than fine dust in two of the three soils evaluated; and (iii) certain bacteria were more predominant in fine dust (, , and ) than coarse sediment ( and ), revealing different locations and niches of bacteria in soil, which, depending on wind erosion processes, can have important implications on the soil sustainability and functioning. Infrared spectroscopy showed that wind erosion preferentially removes particular kinds of C from the soil that are lost via fine dust. Our study shows that eroded sediments remove the active labile organic soil particulates containing key microorganisms involved in soil biogeochemical processes, which can have a negative impact on the quality and functioning of the source soil.

Effect of dihydrotestosterone on gastrointestinal tract of male Alzheimer's disease transgenic mice.

The cause of Alzheimer's disease (AD) is still unknown. While research contributions identifying brain as locus of the disease is growing, evidence of severely impaired gastrointestinal (GI) functions with ageing too is accumulating, there is an equal dearth of information on GI tract in AD condition. The aim of this study was to assess the molecular, histological, morphological and microflora alterations of GI tract in male Alzheimer's transgenic mice. The present study also investigates the effect of dihydrotestosterone (DHT) treatment (1 mg/kg) on AD mice. Histoarchitecture data revealed a significant decrease in the villi number, muscular layer thickness, villi length, width, crypt length, enterocyte length and nuclei length. A shift in colon feces microbial community composition was observed by fatty acid methyl ester analysis. Amyloid precursor protein (APP) expression levels in intestine significantly increased in AD mice revealing its toxicity. DHT treatment attenuated the effect caused by AD on GI morphometrics, APP expression and colon micro flora population. These results for the first time reveal the quantitative and qualitative characteristics of GI tract in male Alzheimer's disease transgenic mice.

Mid-Infrared and near-infrared spectral properties of mycorrhizal and non-mycorrhizal root cultures.

We investigated the Fourier-transformed mid-infrared (MIR) and near-infrared (NIR) spectroscopic properties of mycorrhizal (M) and non-mycorrhizal (NM) carrot roots with the goal of finding infrared markers for colonization by arbuscular mycorrhizal (AM) fungi. The roots were cultured with or without the AM fungus Glomus intraradices under laboratory conditions. A total of 50 M and NM samples were produced after pooling subsamples. The roots were dried, ground, and scanned separately for the NIR and MIR analyses. The root samples were analyzed for fatty acid composition in order to confirm mycorrhizal infection and to determine the presence of fatty acid markers. Besides the roots, fatty acid standards, pure cultures of saprophytic fungi, and chitin were also scanned in order to identify spectral bands likely to be found in M samples. Principal components analysis (PCA) was used to illustrate spectral differences between the M and NM root samples. The NIR analysis achieved good resolution with the raw spectral data and no pretreatment was needed to obtain good resolution in the PCA analysis of the NIR data. Standard normal variate and detrending pretreatment improved the resolution between M and NM in the MIR range. The PCA loadings and/or the spectral subtraction of selected samples showed that M roots are characterized by absorbances at or close to 400 cm(-1), 1100-1170 cm(-1), 1690 cm(-1), 2928 cm(-1), and 5032 cm(-1). The NM samples had characteristic absorbances at or near 1734 cm(-1), 3500 cm(-1), 4000 cm(-1), 4389 cm(-1), and 4730 cm(-1). Some of the bands that differentiate M from NM roots are prominent in the spectra of pure fungal cultures, chitin, and fatty acids. Our results show that mycorrhizal and nonmycorrhizal root tissues can be differentiated via MIR and NIR spectra with the advantage that the same samples can then be used for other analyses.

Linking microbial community structure and function to seasonal differences in soil moisture and temperature in a Chihuahuan desert grassland.

Global and regional climate models predict higher air temperature and less frequent, but larger precipitation events in arid regions within the next century. While many studies have addressed the impact of variable climate in arid ecosystems on plant growth and physiological responses, fewer studies have addressed soil microbial community responses to seasonal shifts in precipitation and temperature in arid ecosystems. This study examined the impact of a wet (2004), average (2005), and dry (2006) year on subsequent responses of soil microbial community structure, function, and linkages, as well as soil edaphic and nutrient characteristics in a mid-elevation desert grassland in the Chihuahuan Desert. Microbial community structure was classified as bacterial (Gram-negative, Gram-positive, and actinomycetes) and fungal (saprophytic fungi and arbuscular mycorrhiza) categories using (fatty acid methyl ester) techniques. Carbon substrate use and enzymic activity was used to characterize microbial community function annually and seasonally (summer and winter). The relationship between saprophytic fungal community structure and function remained consistent across season independent of the magnitude or frequency of precipitation within any given year. Carbon utilization by fungi in the cooler winter exceeded use in the warmer summer each year suggesting that soil temperature, rather than soil moisture, strongly influenced fungal carbon use and structure and function dynamics. The structure/function relationship for AM fungi and soil bacteria notably changed across season. Moreover, the abundance of Gram-positive bacteria was lower in the winter compared to Gram-negative bacteria. Bacterial carbon use, however, was highest in the summer and lower during the winter. Enzyme activities did not respond to either annual or seasonal differences in the magnitude or timing of precipitation. Specific structural components of the soil microbiota community became uncoupled from total microbial function during different seasons. This change in the microbial structure/function relationship suggests that different components of the soil microbial community may provide similar ecosystem function, but differ in response to seasonal temperature and precipitation. As soil microbes encounter increased soil temperatures and altered precipitation amounts and timing that are predicted for this region, the ability of the soil microbial community to maintain functional resilience across the year may be reduced in this Chihuahuan Desert ecosystem.

Memory and learning behavior in mice is temporally associated with diet-induced alterations in gut bacteria.

The ability of dietary manipulation to influence learning and behavior is well recognized and almost exclusively interpreted as direct effects of dietary constituents on the central nervous system. The role of dietary modification on gut bacterial populations and the possibility of such microbial population shifts related to learning and behavior is poorly understood. The purpose of this study was to examine whether shifts in bacterial diversity due to dietary manipulation could be correlated with changes in memory and learning. Five week old male CF1 mice were randomly assigned to receive standard rodent chow (PP diet) or chow containing 50% lean ground beef (BD diet) for 3 months. As a measure of memory and learning, both groups were trained and tested on a hole-board open field apparatus. Following behavioral testing, all mice were sacrificed and colonic stool samples collected and analyzed by automated rRNA intergenic spacer analysis (ARISA) and bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) approach for microbial diversity. Results demonstrated significantly higher bacterial diversity in the beef supplemented diet group according to ARISA and bTEFAP. Compared to the PP diet, the BD diet fed mice displayed improved working (P=0.0008) and reference memory (P<0.0001). The BD diet fed animals also displayed slower speed (P<0.0001) in seeking food as well as reduced anxiety level in the first day of testing (P=0.0004). In conclusion, we observed a correlation between dietary induced shifts in bacteria diversity and animal behavior that may indicate a role for gut bacterial diversity in memory and learning.

Molecular mapping and characterization of BLMC, a locus for profuse wax (bloom) and enhanced cuticular features of Sorghum (Sorghum bicolor (L.) Moench.).

Sorghum is distinct from other cereal crops due to its ability to produce profuse amount of epicuticular wax (EW or bloom) on its culm and leaves along with less permeable cuticle which are considered to be important traits contributing to abiotic stress tolerance. Here, we report the molecular mapping and characterization of BL OO M-C UTICLE (BLMC), a locus associated with production of profuse wax, using a mutant mapping population developed from a cross between BTx623 (wild type with profuse wax) and KFS2021 (a mutant with greatly reduced wax). The F2 progenies were genotyped using known and newly developed microsatellite markers to establish a molecular map of BLMC. The locus mapped to a 3.6-centimorgans (cM) interval in the terminal end of sorghum chromosome 10 with flanking markers Xsbarslbk10.47 and Xcup42. Targeted mapping delimited BLMC to as small as 0.7 cM region and facilitated identification of three cosegregating markers with the trait. The BLMC region corresponds to approximately 153,000 bp and candidate genes identified include among others an acyl CoA oxidase (a gene involved in lipid and wax biosynthesis) and seven other putative transcripts. Phenotypic characterization showed that in addition to disrupting the EW production, BLMC mutation reduced culm and leaf cuticle, increased plant death rating in the field at anthesis and significantly reduced the C:28 to C:30 free fatty acid fractions of culm and leaf EW. These results clearly support the important role of BLMC in the expression of profuse wax and enhanced cuticular features of sorghum. Genetic mapping of BLMC opened avenues for identification of genes involved in the cuticle/wax pathway of sorghum and their application for improvement of abiotic stress tolerance.

Soil microbial community response to drought and precipitation variability in the Chihuahuan Desert.

Increases in the magnitude and variability of precipitation events have been predicted for the Chihuahuan Desert region of West Texas. As patterns of moisture inputs and amounts change, soil microbial communities will respond to these alterations in soil moisture windows. In this study, we examined the soil microbial community structure within three vegetation zones along the Pine Canyon Watershed, an elevation and vegetation gradient in Big Bend National Park, Chihuahuan Desert. Soil samples at each site were obtained in mid-winter (January) and in mid-summer (August) for 2 years to capture a component of the variability in soil temperature and moisture that can occur seasonally and between years along this watershed. Precipitation patterns and amounts differed substantially between years with a drought characterizing most of the second year. Soils were collected during the drought period and following a large rainfall event and compared to soil samples collected during a relatively average season. Structural changes within microbial community in response to site, season, and precipitation patterns were evaluated using fatty acid methyl ester (FAME) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analyses. Fungal FAME amounts differed significantly across seasons and sites and greatly outweighed the quantity of bacterial and actinomycete FAME levels for all sites and seasons. The highest fungal FAME levels were obtained in the low desert scrub site and not from the high elevation oak-pine forests. Total bacterial and actinomycete FAME levels did not differ significantly across season and year within any of the three locations along the watershed. Total bacterial and actinomycete FAME levels in the low elevation desert-shrub and grassland sites were slightly higher in the winter than in the summer. Microbial community structure at the high elevation oak-pine forest site was strongly correlated with levels of NH4+-N, % soil moisture, and amounts of soil organic matter irrespective of season. Microbial community structure at the low elevation desert scrub and sotol grasslands sites was most strongly related to soil pH with bacterial and actinobacterial FAME levels accounting for site differences along the gradient. DGGE band counts of amplified soil bacterial DNA were found to differ significantly across sites and season with the highest band counts found in the mid-elevation grassland site. The least number of bands was observed in the high elevation oak-pine forest following the large summer-rain event that occurred after a prolonged drought. Microbial responses to changes in precipitation frequency and amount due to climate change will differ among vegetation zones along this Chihuahuan Desert watershed gradient. Soil bacterial communities at the mid-elevation grasslands site are the most vulnerable to changes in precipitation frequency and timing, while fungal community structure is most vulnerable in the low desert scrub site. The differential susceptibility of the microbial communities to changes in precipitation amounts along the elevation gradient reflects the interactive effects of the soil moisture window duration following a precipitation event and differences in soil heat loads. Amounts and types of carbon inputs may not be as important in regulating microbial structure among vegetation zones within in an arid environment as is the seasonal pattern of soil moisture and the soil heat load profile that characterizes the location.