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Graphical abstract, Impact of environmental perturbations i.e., nitrogen (N), phosphorus (P), potassium (K), and rice straw (Rs) on the dynamics of soil bacterial and archaeal communities are multifactor dependent and seeks a contemporary approach to study underlying mechanisms. The current study investigates the effect of pure and mixed fertilizers on soil physicochemical properties, the microbial community structure, and their functional metabolic predictions. It involved amendments with distinct combinations of N as C(H2N)2O, P and K as KH2PO4, K as KCl, and Rs in paddy soil microcosms with concentrations common in rice fields agriculture. Soil pH, electrical conductivity (EC), total carbon (TC), total nitrogen (TN), organic matter (OM), available K (AK), and total extractable P (TEP) were evaluated. To comprehend community variation and functional predictions, 16S rRNA-based high throughput sequencing (HTS) and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) were employed, respectively. Our findings showed enhanced community richness and diversity in all amendments compared to control. Proteobacteria, Actinobacteria, and Firmicutes were dominant bacterial phyla. Regarding relative abundance, Chloroflexi, Bacteroidetes, and Verrucomicrobia showed positive while Actinobacteria, Acidobacteria, and Gemmatimonadetes showed negative trends compared to controls. Thaumarchaeota and Euryarchaeota were dominant archaeal phyla and exhibited increasing and decreasing trends, respectively. The PICRUSt analysis indicated functional prediction more towards amino acid, carbohydrate, energy, and lipid metabolism while less towards others. Concerning energy metabolism, most and least responsive treatments were KP and controls, respectively. These outcomes enhanced our understanding regarding soil quality, fertilizer composition and application, and functional metabolomics of archaea and bacteria.

Sustainable agricultural practices such as reduced tillage and optimized fertilization may have potential to improve soil health and increase availability of plant nutrients and yields. However, there is very little information relating soil quality or health to crop productivity, particularly under farmer management. Therefore, the objective was to investigate the effects of two contrasting approaches to crop fertility management on crop productivity, soil test measurements, and soil enzyme activity as integrative measures of soil health. A three year study was conducted at on-farm sites in Ohio, Illinois, and Iowa where topsoil (0-15 cm) and crop yield of Zea mays L. (corn) and Glycine max. (L.) Merr. (soybean) rotations were collected from two contrasting fertility management systems. The two contrasting approaches tested were the Maximum Farming System (MFSyst) and a more Conventional system (Conv) that differ in approaches to tillage and the frequency of fertilizer applications during the growing season. The MFSyst approach resulted in significantly higher yields, soil nutrient test levels along with β-glucosidase (GLU) and arylsulfatase (ARYL) which are sensitive soil health indicators. Nitrogen use efficiency (NUE) of corn was significantly elevated by nearly 18%, corn yield correlated with GLU activities, and soil test phosphorous (P) levels were reduced by over 50% using the MFSyst approach. These results indicate that improvements in soil health detected by soil GLU and ARYL enzyme activities are associated with significant improvements in soil quality and crop productivity.

The skin microbiota is import for body protection. Here we present the first comprehensive analysis of the volatile organic compound (VOC) profiles of typical skin-resident corynebacterial and staphylococcal species. The VOC profile of Staphylococcus schleiferi DSMZ 4807 was of particular interest as it is dominated by two compounds, 3-(phenylamino)butan-2-one and 3-(phenylimino)butan-2-one (schleiferon A and B, respectively). Neither of these has previously been reported from natural sources. Schleiferon A and B inhibited the growth of various Gram-positive species and affected two quorum-sensing-dependent phenotypes – prodigiosin accumulation and bioluminescence – of Gram-negative bacteria. Both compounds were found to inhibit the expression of prodigiosin biosynthetic genes and stimulate the expression of prodigiosin regulatory genes pigP and pigS. This study demonstrates that the volatile schleiferons A and B emitted by the skin bacterium S. schleiferi modulate differentially and specifically its interactions with members of diverse bacterial communities. A network of VOC-mediated interspecies interactions and communications must be considered in the establishment of the (skin) microbiome and both compounds are interesting candidates for further investigations to better understand how VOCs emitted by skin bacteria influence and modulate the local microbiota and determine whether they are relevant to antibiotic and anti-virulence therapies.

In commercial agriculture, populations and interactions of rhizosphere microflora are potentially affected by the use of specific agrichemicals, possibly by affecting gene expression in these organisms. To investigate this, we examined changes in bacterial gene expression within the rhizosphere of glyphosate-tolerant corn (Zea mays) and soybean (Glycine max) in response to long-term glyphosate (PowerMAX™, Monsanto Company, MO, USA) treatment. A long-term glyphosate application study was carried out using rhizoboxes under greenhouse conditions with soil previously having no history of glyphosate exposure. Rhizosphere soil was collected from the rhizoboxes after four growing periods. Soil microbial community composition was analyzed using microbial phospholipid fatty acid (PLFA) analysis. Total RNA was extracted from rhizosphere soil, and samples were analyzed using RNA-Seq analysis. A total of 20–28 million bacterial sequences were obtained for each sample. Transcript abundance was compared between control and glyphosate-treated samples using edgeR. Overall rhizosphere bacterial metatranscriptomes were dominated by transcripts related to RNA and carbohydrate metabolism. We identified 67 differentially expressed bacterial transcripts from the rhizosphere. Transcripts downregulated following glyphosate treatment involved carbohydrate and amino acid metabolism, and upregulated transcripts involved protein metabolism and respiration. Additionally, bacterial transcripts involving nutrients, including iron, nitrogen, phosphorus, and potassium, were also affected by long-term glyphosate application. Overall, most bacterial and all fungal PLFA biomarkers decreased after glyphosate treatment compared to the control. These results demonstrate that long-term glyphosate use can affect rhizosphere bacterial activities and potentially shift bacterial community composition favoring more glyphosate-tolerant bacteria.

N-Acylhomoserine lactones are autoinducers of quorum sensing (QS) in Gram-negative bacteria. We exploit here the role of structurally related (beta)-lactones in the inhibition of Vibrio harveyi bioluminescence and identify a derivative with nanomolar potency. Surprisingly, QS was not affected and combined proteomic/biochemical studies revealed insights into the cellular mode of action.

Quorum sensing (QS) is a communication process that enables a bacterial population to coordinate and synchronize specific behaviors. The bioluminescent marine bacterium Vibrio harveyi integrates three autoinducer (AI) signals into one quorum-sensing cascade comprising a phosphorelay involving three hybrid sensor kinases: LuxU; LuxO, an Hfq/small RNA (sRNA) switch; and the transcriptional regulator LuxR. Using a new set of V. harveyi mutants lacking genes for the AI synthases and/or sensors, we assayed the activity of the quorum-sensing cascade at the population and single-cell levels, with a specific focus on signal integration and noise levels. We found that the ratios of kinase activities to phosphatase activities of the three sensors and, hence, the extent of phosphorylation of LuxU/LuxO are important not only for the signaling output but also for the degree of noise in the system. The pools of phosphorylated LuxU/LuxO per cell directly determine the amounts of sRNAs produced and, consequently, the copy number of LuxR, generating heterogeneous quorum-sensing activation at the single-cell level. We conclude that the ability to drive the heterogeneous expression of QS-regulated genes in V. harveyi is an inherent feature of the architecture of the QS cascade. IMPORTANCE V. harveyi possesses one of the most complex quorum-sensing (QS) cascades known, using three different autoinducers (AIs) to control the induction of, e.g., bioluminescence, virulence factors, and biofilm and exoprotease production. We constructed various V. harveyi mutants to study the impact of each component and subsystem of the QS signaling cascade on QS activation at the population and single-cell levels. We found that the output was homogeneous only in the presence of all AIs. In the absence of any one AI, QS activation varied from cell to cell, resulting in phenotypic heterogeneity. This study elucidates a molecular design principle which enables a tightly integrated signaling cascade to control the expression of diverse phenotypes within a genetically homogeneous population.

Quorum sensing (QS) is a process enabling a bacterial population to communicate via small molecules called autoinducers (AIs). This intercellular communication process allows single cells to synchronize their behavior within a population. The marine bacterium Vibrio harveyi ATCC BAA-1116 channels the information of three AI signals into one QS cascade. Three receptors perceive these AIs, the hybrid histidine kinases LuxN, Lux(P)Q and CqsS, to transduce the information to the histidine phosphotransfer (HPt) protein LuxU via phosphorelay, and finally to the response regulator LuxO. Hence, the level of phosphorylated LuxO depends on the AI concentrations. The phosphorylated LuxO (P-LuxO) controls the expression of small regulatory RNAs (sRNAs), which together with the RNA chaperon Hfq, destabilize the transcript of the master regulator luxR. LuxR is responsible for the induction and repression of several genes (e.g., for bioluminescence, exoprotease and siderophore production). In vivo studies with various mutants have demonstrated that the ratio between kinase and phosphatase activities of the individual QS receptors and therefore the P-LuxO/LuxO ratio is crucial not only for the output strength but also for the degree of noise. This study was undertaken to better understand the inherent design principles of this complex signaling cascade, which allows sensing and integration of different signals, but also the differentiated output in individual cells. Therefore, we quantitatively analyzed not only the enzymatic activities, but also the abundance and localization of the three QS receptors. We found that LuxN presents the highest capacity to phosphorylate LuxU, while the phosphatase activity was comparable to LuxQ and CqsS in vitro. In whole cells the copy number of LuxN was higher than that of LuxQ and CqsS, and further increased in the late exponential growth phase. Microscopy experiments indicate that LuxN and LuxQ form independent clusters. Altogether, these results suggest, that the three QS receptors act in parallel, and V. harveyi has developed with LuxN the most dynamic sensing range for HAI-1, the species-specific AI.

Anaerobic methane oxidizing organisms, including sulfate dependent archaea (SAMO), nitrite dependent bacteria (n-damo), and nitrate archaea (n-damo), may collaborate with anaerobic ammonia oxidizers (anammox) bacteria in wetlands to remove inorganic nitrogen. The objective was to examine the structure and abundance of these organisms and their response to substrate inputs (sulfate, nitrate, or nitrite) in two wetlands of contrasting properties: a natural wetland and a constructed wetland to treat swine manure. No SAMO archaea were detected in either wetland. For n-damo bacteria, Ca. Methylomirabilis oxyfera dominated the natural wetland, while Clade 2 dominated the constructed wetland. For n-damo archaea, Clade 1 dominated the constructed wetland, while Clade 3 dominated the natural wetland. For anammox bacteria, Ca. Brocadia dominated both the natural wetland and the constructed wetland. Generally, the natural wetland contained higher gene abundance and more diversity of these three microorganisms than the constructed wetland, which could be due to high ammonium concentrations in the constructed wetland, forcing selections of genotypes to a narrow range of microorganisms. A slurry incubation experiment showed that both n-damo archaea and anammox bacteria increased over time in the constructed wetland sediment, indicating these two microorganisms might cooperate to complete the denitrification process from nitrate to dinitrogen gas.

The use of switchgrass (Panicum virgatum L.) as an energy crop has gained great importance in past two decades due to its high biomass yields on marginal lands with low agricultural inputs and low maintenance requirements. Information on the allocation of photosynthetically fixed C in the switchgrass-soil system is important to under stand the C flow and to quantify the sequestration of C in soils. The allocation of 13 C labeled photosynthates in shoot, root, soil, and in microbial biomass carbon (MBC) of rhizosphere and bulk soil of 45 days old, greenhouse grown-switchgrass was examined during 20 days 13 C-CO 2 pulse labeling period. The total 13 C recovered in the plant-soil system varied from 79% after 1 day to 42% after 20 days of labeling. After labeling, 54%, 40%, and 6% excess 13 C resided in shoot, root and soil, respectively on day 1; 27%, 61% and 11%, respectively on day 5 and 20%, 63% and 17%, respectively day 20 after labeling. The maximum incorporation of 13 C from roots into the MB of rhizosphere soil occurred within the first 24 h of labeling. The excess 13 C values of rhizosphere soil and rhizosphere MBC were significantly higher than excess 13 C values of bulk soil and the bulk soil MBC, respectively. The propor tion of excess 13 C in soil as MBC declined from 92 to 15% in rhizosphere soil and from 79 to 18% in bulk soil, for 1 day and 20 days after labeling, respectively. The present study showed the effectiveness of 13 C labeling to examine

Livestock production in Latin America has replaced tropical dry forests with conventional monocultures pastures (CP) that have degraded soils. As an alternative to CP, intensive silvopastoral systems (ISS) have been developed with multi-canopied vegetation that mimics native forest (F). The litter inputs and year-round presence of the tree rhizosphere in ISS, contribute to the formation of “fertile islands,” which is expected to impact biological activity and crop productivity. This study, investigated the impact of the conversion of CP to ISS, as well as the effect of canopy of Prosopis juliflora trees in a chronosequence of ISS (3–15 years) on soil microbial communities and the physicochemical properties of soil. FAME (fatty acid methyl ester) profiles indicated that soil microbial community structure and composition shifted depending on land management systems. CP promoted the dominance of G− bacteria, while ISS chronosequence and F favored actinomycetes and fungal biomass (total and arbuscular mycorrhizal fungi). In addition, soil microbial community (FAME profiles) of ISS chronosequence and F were more similar than with CP. An increase in the Cy/pre FAME ratio in CP suggested that the microbial community was under higher stress. The advantage of including trees in pasture systems was reinforced by the observation that FAME biomarkers, enzymatic activities and nutrient status were significantly higher beneath the canopy of P. juliflora. The results indicate that ISS are viable alternatives for improving soil quality and metabolic function, which is reflected in the significant increase in microbial biomass, FAME biomarkers and enzyme activities compared with CP.

There is widespread interest in the renewable biofuel potential of Jatropha curcas L., a shrub that exists under indigenous conditions in India. Following oil extraction from seeds, the remaining shell and cake residue can be used as a soil amendment. Microbial decomposition of organic residues can improve the quality of soils, but little is known about Jatropha as a soil amendment. Therefore, the objective of this study was to determine the influence of Jatropha residue on soil microbial community structure during decomposition. Soil microcosms amended with Jatropha leaves, cake, or fruit shell or an unamended control were incubated in the laboratory and destructively sampled at 3, 10, 20, 40, and 60 days. At each sampling, soil microbial communities were analyzed using fatty acid methyl ester (FAME) profiles, and enzyme assays performed for β-glucosidase, cellulase, and urease. Microbial biomass (FAMEtot) and bacterial and fungal FAME concentrations were significantly higher in cake-amended soil compared with other treatments. Averaged across all treatments, FAMEtot and fungal and bacterial FAMEs were highest on Day 3 and subsequently decreased significantly. Higher fungal-to-bacterial FAME ratios were found in residue-amended soils over control, with the highest ratio occurring in fruit shell-amended soil (except Day 3). A significantly lower ratio of the stress indicator (saturated to monounsaturated FAMEs) was found in cake-amended soil compared with other amendments. Fungal, bacterial, and actinomycetes biomarkers were significantly correlated with β-glucosidase and cellulase activities. The study shows that decomposition of Jatropha affected the soil microbial community, differently depending on residue type, but overall had positive effects in promoting the microbial diversity and activity, thus making Jatropha residue a favorable amendment for soils.

The benefits of cover crops within crop rotations are well documented, but information is limited on using cover crops for forage within midwestern United States cropping systems, especially under no-tillage management. Our objective was to evaluate plant, animal, and soil responses when integrating winter cover crop forages into no-till corn (Zea mays L.) silage production. Three cover crop treatments were established no-till after corn silage in September 2006 and 2007 at Columbus, OH: annual ryegrass (Lolium multiflorum L.), a mixture of winter rye (Secale cereale L.) and oat (Avena sativa L.), and no cover crop. Total forage yield over autumn and spring seasons was 38 to 73% greater (P ≤ 0.05) for oat + winter rye than for annual ryegrass. Soil penetration resistance (SPR) in May 2007 was 7 to 15% greater (P ≤ 0.10) in the grazed cover crops than in the nongrazed no cover crop treatment; however, subsequent silage corn yield did not differ among treatments, averaging 10.4 Mg ha -1 in August 2007. Compared with the no cover crop treatment, cover crops had three- to fivefold greater root yield, threefold greater soil microbial biomass (MB) in spring 2008, and 23% more particulate organic carbon (POC) concentrations in the 0- to 15-cm soil depth. Integration of forage cover crops into no-till corn silage production in Ohio can provide supplemental forage for animal feed without detrimental effects on subsequent corn silage productivity, with the added benefit of increasing labile soil C.

Phages are bacteria targeting viruses and represent the most abundant biological entities on earth. Marine environments are exceptionally rich in bacteriophages, harboring a total of 4x10(30) viruses. Nevertheless, marine phages remain poorly characterized. Here we describe the identification of intact prophage sequences in the genome of the marine gamma-proteobacterium Vibrio campbellii ATCC BAA-1116 (formerly known as V. harveyi ATCC BAA-1116), which presumably belong to the family of Myoviridae. One prophage was found on chromosome I and shows significant similarities to the previously identified phage Phi HAP-1. The second prophage region is located on chromosome II and is related to Vibrio phage kappa. Exposure of V. campbellii to mitomycin C induced the lytic cycle of two morphologically distinct phages and, as expected, extracellular DNA from induced cultures was found to be specifically enriched for the sequences previously identified as prophage regions. Heat stress (50 degrees C, 30 min) was also found to induce phage release in V. campbellii. Notably, promoter activity of two representative phage genes indicated heterogeneous phage induction within the population.

A long-standing dilemma for soil microbial assays is how best to store soil samples between sampling and analysis. We studied the effects of sample handling and storage on methods used to determine soil microbial biomass, structure, and function. For this study, one forest soil (Gilpin), and two agricultural soils (Granby and Hoytville) were selected with five commonly used sample pretreatments: (i) fresh soil; (ii) air drying for 14 d followed by rewetting (65% water-holding capacity) and incubation (25°C) for 14 d (D/R); (iii) 28 d at 4°C; (iv) 28 d at -20°C; and (v) 28 d at -80°C. Immediately after pretreatments, soils were analyzed for fatty acid methyl esters (FAMEs), total DNA (tDNA), seven enzyme activities, microbial biomass C, and respiration. Drying and rewetting significantly reduced microbial biomass, respiration, most enzyme activities, tDNA, and total FAME concentrations compared with fresh soil in all three soils. The percentage of fungal FAME markers and two enzyme assays were unaffected by 4°C storage in all soils, and microbial biomass C was unchanged in Hoytville and Gilpin soil at -20 and -80°C. Total DNA was unchanged in the Granby soil at -80°C, and in the Hoytville soil at both -20 and -80°C compared with fresh soil. Total FAME was reduced by all storage treatments in all three soils. We concluded that storage should be avoided whenever possible, particularly for extraction of FAME and total DNA, but that 4 or -20°C is the best storage method for FAME analysis, and -80°C is preferable for DNA analysis. Microbial biomass C and enzyme activities were least affected when stored at 4 or -20°C. The D/R treatment was the least desirable soil preparation method for microbial analyses, and we recommend that this pretreatment be avoided.

Glyphosate is one of the most widely used herbicides in agriculture with predictions that 1.35millionmetric tons will be used annually by 2017. With the advent of glyphosate tolerant (GT) cropping more than 10years ago, there is now concern for non-target effects on soil microbial communities that has potential to negatively affect soil functions, plant health, and crop productivity. Although extensive research has been done on short-term response to glyphosate, relatively little information is available on long-term effects. Therefore, the overall objective was to investigate shifts in the rhizosphere bacterial community following long-term glyphosate application on GT corn and soybean in the greenhouse. In this study, rhizosphere soil was sampled from rhizoboxes following 4 growth periods, and bacterial community composition was compared between glyphosate treated and untreated rhizospheres using next-generation barcoded sequencing. In the presence or absence of glyphosate, corn and soybean rhizospheres were dominated by members of the phyla Proteobacteria, Acidobacteria, and Actinobacteria. Proteobacteria (particularly gammaproteobacteria) increased in relative abundance for both crops following glyphosate exposure, and the relative abundance of Acidobacteria decreased in response to glyphosate exposure. Given that some members of the Acidobacteria are involved in biogeochemical processes, a decrease in their abundance could lead to significant changes in nutrient status of the rhizosphere. Our results also highlight the need for applying culture-independent approaches in studying the effects of pesticides on the soil and rhizosphere microbial community.

Vibrio is a model organism for the study of quorum sensing (QS) signaling and is used to identify QS-interfering drugs. Naturally occurring fimbrolides are important tool compounds known to affect QS in various organisms; however, their cellular targets have so far remained elusive. Here we identify the irreversible fimbrolide targets in the proteome of living V. harveyi and V. campbellii via quantitative mass spectrometry utilizing customized probes. Among the major hits are two protein targets with essential roles in Vibrio QS and bioluminescence. LuxS, responsible for autoinducer 2 biosynthesis, and LuxE, a subunit of the luciferase complex, were both covalently modified at their active-site cysteines leading to inhibition of activity. The identification of LuxE unifies previous reports suggesting inhibition of bioluminescence downstream of the signaling cascade and thus contributes to a better mechanistic understanding of these QS tool compounds.

Arsenic (As) and cadmium (Cd) in soils can affect soil microbial function and community composition and, therefore, may have effects on soil ecosystem functioning. The aim of our study was to assess the effects of long-term As and Cd contamination on soil microbial community composition and soil enzyme activities. We analyzed soils that have been contaminated 25 years ago and at present still show enhanced levels of either As, 18 and 39 mg kg−1, or Cd, 34 and 134 mg kg−1. Soil without heavy metal addition served as control. Polymerase chain reaction (PCR) followed by denaturing gradient gel electrophoresis (DGGE) showed that bacterial community composition in As and Cd contaminated soils differed from that in the control soil. The same was true for the microbial community composition assessed by analysis of respiratory quinones. Soil fungi and Proteobacteria appeared to be tolerant towards As and Cd, while other groups of bacteria were reduced. The decline in alkaline phosphatase, arylsulphatase, protease and urease activities in the As- and Cd-contaminated soils was correlated with a decrease of respiratory quinones occuring in Actinobacteria and Firmicutes. Xylanase activity was unaffected or elevated in the contaminated soils which was correlated with a higher abundance of fungal quinones, and quinones found in Proteobacteria.

The production of biofuels from the low-input energy crops, switchgrass (Panicum virgatumL.) and jatropha (Jatropha curcasL.), is a sustainable approach that can provide more usable energy and environmental benefits than food-based biofuels. Plant rhizosphere affects the microbial community structure due to variations in root exudation rates and residue chemistry. The objective of this investigation was to determine the profiles of microbial communities associated with rhizosphere and bulk soils of switchgrass or jatropha using phospholipid fatty acid (PLFA) analysis and length heterogeneity PCR (LH-PCR). Switchgrass soil contained a significantly (P<0.05) higher abundance of Gram-positive (i14:0, i15:0, a15:0), Gram-negative (16:1ω5c, 16:1ω7c, 18:1ω5c), and saturated (14:0, 15:0) PLFAs compared to jatropha soil, whereas jatropha had a higher abundance of fungal (18:2ω6, 9c), 18:1ω9c, 20:1ω9c, and 18:0 PLFAs compared to switchgrass soil. Irrespective of plant type, rhizosphere soil contained a significantly (P<0.05) higher abundance of saturated PLFAs (16:0, 18:0, 20:0), actinomycetes (10Me17:0), and fungal (18:2ω6, 9c) PLFAs compared to bulk soil; whereas bulk soil had higher abundance of saturated (14:0), Gram-negative (16:1ω9c, 16:1ω5c, 16:1ω7c), and 18:1ω9c PLFAs compared to rhizosphere soil. Multivariate principle component analysis of PLFAs and LH-PCR percent relative peak areas successfully differentiated the microbial communities of rhizosphere and bulk soils of switchgrass and jatropha.