Microbial communities of continuously cropped, irrigated rice fields

Rotations improve the diversity of rhizosphere soil bacterial communities, enzyme activities and tomato yield

The use of rotations is an effective strategy to control crop diseases and improve plant health. The soil bacterial communities in the rhizosphere are highly important for maintaining soil productivity. However, the composition and structure of soil bacterial communities in the rotations of vegetable crops remain unclear. In this study, we explored the bacterial diversity and community structure of the tomato rhizosphere, including enzyme activities, yield, and fruit quality, under three different cropping systems: tomato-tomato (Solanum lycopersicum) continuous cropping (TY1), eggplant (Solanum melongena)-tomato rotation (TY2) and arrowhead (Sagittaria trifolia)-tomato rotation (TY3). The composition and diversity of the rhizosphere bacterial communities differed significantly. The diversity was more in the TY2 and TY3 treatments than those in the TY1 treatment. Chujaibacter and Rhodanobacter were two predominant and unique strains detected only in TY1, while the relative abundances of Curvibacter and Luteimonas were the highest in TY2 and TY3, respectively. Moreover, Lysobacter was a relatively abundant type of biocontrol bacterium found only in the TY3 treatment, which could contribute to alleviating the obstacle of tomato continuous cropping. Compared with the TY1 treatment, the activities of catalase were significantly higher in the TY2 and TY3 treatments. In addition, compared with TY1, the TY2 and TY3 plots increased the following parameters: tomato yields by 24-46%, total soluble solids by 37-93%, total organic acid by 10-15.7% and soluble protein by 10-21%, while the content of nitrate was significantly reduced by 23%. Altogether, compared with the tomato monoculture, the rotations of tomato with eggplant and arrowhead shifted the rhizosphere bacterial communities and improved the yield and quality of the tomato. Moreover, a tomato rotation, particularly with arrowhead, was an effective way to alleviate the obstacles of continuous cropping.

Rhizosphere Bacterial Community Response to Continuous Cropping of Tibetan Barley

Long-term continuous cropping influences the nutrient of soil and microbiome of the rhizosphere, resulting in the yield decrease of crops. Tibetan barley is a dominant cereal crop cultivated at high altitudes in Tibet. Its growth and yield are negatively affected by continuous cropping; however, the response of the rhizosphere microbial community to continuous cropping remains poorly understood. To address this question, we investigated the bacterial community structure and conducted predictive functional profiling on rhizosphere soil from Tibetan barley monocropped for 2–6 years. The results revealed that long-term continuous cropping markedly decreased total nitrogen and available nitrogen in rhizosphere soil. Illumina high-throughput sequencing of 16S rRNA genes indicated that the bacterial community was altered by continuous cropping; operational taxonomic units (OTUs), Shannon index, and Faith Phylogenetic Diversity decreased with increasing monocropping duration. Relative abundances of family Pseudomonadaceae, Cytophagaceae, and Nocardioidaceae were significantly increased, while those of Chitinophagaceae and Sphingomonadaceae were significantly decreased (all p < 0.05). Besides, continuous cropping significantly increased the abundance of bacteria associated with chemoheterotrophy, aromatic compound degradation, and nitrate reduction (p < 0.05). Generalized boosted regression model analysis indicated that total nitrogen was the most important contributor to the bacterial community diversity, indicating their roles in shaping the rhizosphere bacterial community during continuous cropping. Overall, continuous cropping had a significant impact on the structure of bacterial communities in rhizosphere soil of Tibetan barley, and these results will improve our understanding of soil bacterial community regulation and soil health maintenance in Tibetan barley farm systems.

Compound-specific 13 C stable isotope probing confirms synthesis of polyhydroxybutyrate by soil bacteria

RATIONALE

Many bacteria synthesize carbon (C) and energy storage compounds, including water-insoluble polyester lipids composed mainly or entirely of poly(3-hydroxybutyrate) (PHB). Despite the potential significance of C and energy storage for microbial life and C cycling, few measurements of PHB in soil have been reported.

METHODS

A new protocol was implemented, based on an earlier sediment extraction and derivatization procedure, with quantification by gas chromatography/mass spectrometry (GC/MS) and ¹³ C-isotopic analysis by GC/combustion/isotope ratio mass spectrometry (GC/C/IRMS).

RESULTS

The PHB content was 4.3 μg C g^-1 in an agricultural soil and 1.2 μg C g^-1 in a forest topsoil. This was an order of magnitude more PHB than obtained by the existing extraction method, suggesting that native PHB in soil has been previously underestimated. Addition of glucose increased the PHB content by 135% and 1,215% over 5 days, with the largest increase in the relatively nutrient-poor forest soil. In the agricultural soil, 68% of the increase was derived from added ¹³ C-labeled glucose, confirming synthesis of PHB from glucose for the first time in soil.

CONCLUSIONS

The presence and responsiveness of PHB in both these contrasting soils show that PHB could provide a useful indicator of bacterial nutritional status and unbalanced growth. Microbial storage could be important to C and nutrient cycling and be a widespread strategy in the life of soil bacteria. The presented method offers new insight into the significance of this compound in soil.

Microbial lipid biomarkers detected in deep subsurface black shales

Evidence for microbes has been detected in extreme subsurface environments as deep as 2.5 km with temperatures as high as 90 °C, demonstrating that microbes can adapt and survive extreme environmental conditions. Deep subsurface shales are increasingly exploited for their energy applications, thus characterizing the prevalence and role of microbes in these ecosystems essential for understanding biogeochemical cycles and maximizing production from hydrocarbon-bearing formations. Here, we describe the distribution of bacterial ester-linked phospholipid fatty acids (PLFA) and diglyceride fatty acids (DGFA) in sidewall cores retrieved from three distinct geologic horizons collected to 2275 m below ground surface in a Marcellus Shale well, West Virginia, USA. We examined the abundance and variety of PLFA and DGFA prior to energy development within and above the Marcellus Shale Formation into the overlying Mahantango Formation of the Appalachian Basin. Lipid biomarkers in the cores suggest the presence of microbial communities comprising Gram (+), Gram (-) as well as stress indicative biomarkers. Microbial PLFA and DGFA degradation in the subsurface can be influenced by stressful environmental conditions associated with the subsurface. The PLFA concentration and variety were higher in the transition zone between the extremely low permeability Marcellus Shale Formation and the more permeable Mahantango Formation. In contrast to this distribution, more abundant and diverse DGFA membrane profiles were associated with the Mahantango Formation. The stress indicative biomarkers like the trans-membrane fatty acids, oxiranes, keto-, and dimethyl lipid fatty acids were present in all cores, potentially indicating that the bacterial communities had experienced physiological stress or nutrient deprivation during or after deposition. The DGFA profiles expressed more stress indicative biomarkers as opposed to the PLFA membrane profiles. These findings suggest the probable presence of indigenous microbial communities in the deep subsurface shale and also improves our understanding of microbial survival mechanisms in ancient deep subsurface environments.

Composted Cattle Manure Increases Microbial Activity and Soil Fertility More Than Composted Swine Manure in a Submerged Rice Paddy

Livestock waste composts with minimum inorganic fertilizer as a soil amendment in low-input intensive farming are a feasible agricultural practice to improve soil fertility and productivity and to mitigate soil degradation. The key benefits of the practice rely on the activities of soil microorganisms. However, the role of different livestock composts [composted cattle manure (CCM) vs. composted swine manure (CSM)] on soil microbes, their activities and the overall impact on soil fertility and productivity in a flooded paddy remains elusive. This study compares the effectiveness of CCM and CSM amendment on bacterial communities, activities, nutrient availability, and crop yield in a flooded rice cropping system. We used deep 16S amplicon sequencing and soil enzyme activities to decipher bacterial communities and activities, respectively. Both CCM and CSM amendment significantly increased soil pH, nutrient availability (C, N, and P), microbial biomass, soil enzyme activities indicative for C and N cycles, aboveground plant biomass and grain yield. And the increase in above-mentioned parameters was more prominent in the CCM treatment compared to the CSM treatment. The CCM amendment increased species richness and stimulated copiotrophic microbial groups (Alphaproteobacteria, Betaproteobacteria, and Firmicutes) which are often involved in degradation of complex organic compounds. Moreover, some dominant species (e.g., Azospirillum zeae, Azospirillum halopraeferens, Azospirillum rugosum, Clostridium alkalicellulosi, Clostridium caenicola, Clostridium termitidis, Clostridium cellulolyticum, Magnetospirillum magnetotacticum, Pleomorphomonas oryzae, Variovorax boronicumulans, Pseudomonas xanthomarina, Pseudomonas stutzeri, and Bacillus niacini) which have key roles in plant growth promotion and/or lignocellulose degradation were enhanced under CCM treatment compared to CSM treatment. Multivariate analysis revealed that soil pH and available carbon (C) and nitrogen (N) were the major, while total organic carbon (TOC), total nitrogen (TN), and available phosphorus (P) were the minor drivers of variation in bacterial communities. Overall, our observations suggest that CCM amendment is better than CSM amendment to improve soil fertility and crop yield in a submerged rice cropping system.

Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time

Traditional molecular methods have been used to examine bacterial communities in ginseng-cultivated soil samples in a time-dependent manner. Despite these efforts, our understanding of the bacterial community is still inadequate. Therefore, in this study, a high-throughput sequencing approach was employed to investigate bacterial diversity in various ginseng field soil samples over cultivation times of 2, 4, and 6 years in the first and second rounds of cultivation. We used non-cultivated soil samples to perform a comparative study. Moreover, this study assessed changes in the bacterial community associated with soil depth and the health state of the ginseng. Bacterial richness decreased through years of cultivation. This study detected differences in relative abundance of bacterial populations between the first and second rounds of cultivation, years of cultivation, and health states of ginseng. These bacterial populations were mainly distributed in the classes Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Sphingobacteria. In addition, we found that pH, available phosphorus, and exchangeable Ca⁺ seemed to have high correlations with bacterial class in ginseng cultivated soil.

Arsenite-oxidizing bacteria exhibiting plant growth promoting traits isolated from the rhizosphere of Oryza sativa L.: Implications for mitigation of arsenic contamination in paddies

Arsenite-oxidizing bacteria exhibiting plant growth promoting (PGP) traits can have the advantages of reducing As-uptake by rice and promoting plant growth in As-stressed soil. A gram-positive bacterium Bacillus flexus ASO-6 resistant to high levels of As (32 and 280 mM for arsenite and arsenate, respectively) and exhibiting elevated rates of As(III) oxidation (Vmax=1.34 μM min(-1) 10(-7) cell) was isolated from rhizosphere of rice. The presence of aoxB gene and exhibition of As(III)-oxidase enzyme activity of this strain was observed. The ability of the strain to produce siderophore, IAA, ACC-deaminase and to solubilize phosphate was verified. The rice seed treated with the strain exhibited significantly improved seed germination and seedling vigor compared with the un-inoculated seeds. The bacterial inoculation significantly increased root biomass, straw yield, grain yield, chlorophyll and carotenoid in the rice plant. Moreover, As uptake from root to shoot and As accumulation in straw and grain decreased significantly as a result of the bacterial inoculation. Noteworthy, the inoculation effect is more prominent in non-flooded soil than it is in flooded soil. Owing to its wide action spectrum, this As(III)-oxidizing PGPB could serve as a potential bio-inoculant for mitigation of As in paddies and sustainable rice production in As-contaminated areas.

Dynamic succession of soil bacterial community during continuous cropping of peanut (Arachis hypogaea L.)

Plant health and soil fertility are affected by plant-microbial interactions in soils. Peanut is an important oil crop worldwide and shows considerable adaptability, but growth and yield are negatively affected by continuous cropping. In this study, 16S rRNA gene clone library analyses were used to study the succession of soil bacterial communities under continuous peanut cultivation. Six libraries were constructed for peanut over three continuous cropping cycles and during its seedling and pod-maturing growth stages. Cluster analyses indicated that soil bacterial assemblages obtained from the same peanut cropping cycle were similar, regardless of growth period. The diversity of bacterial sequences identified in each growth stage library of the three peanut cropping cycles was high and these sequences were affiliated with 21 bacterial groups. Eight phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia were dominant. The related bacterial phylotypes dynamic changed during continuous cropping progress of peanut. This study demonstrated that the bacterial populations especially the beneficial populations were positively selected. The simplification of the beneficial microbial communities such as the phylotypes of Alteromonadales, Burkholderiales, Flavobacteriales, Pseudomonadales, Rhizobiales and Rhodospirillales could be important factors contributing to the decline in peanut yield under continuous cropping. The microbial phylotypes that did not successively changed with continuous cropping, such as populations related to Rhizobiales and Rhodospirillales, could potentially resist stress due to continuous cropping and deserve attention. In addition, some phylotypes, such as Acidobacteriales, Chromatiales and Gemmatimonadales, showed a contrary tendency, their abundance or diversity increased with continuous peanut cropping progress. Some bacterial phylotypes including Acidobacteriales, Burkholderiales, Bdellovibrionales, and so on, also were affected by plant age.

Methylmercury production in sediment from agricultural and non-agricultural wetlands in the Yolo Bypass, California, USA

As part of a larger study of mercury (Hg) biogeochemistry and bioaccumulation in agricultural (rice growing) and non-agricultural wetlands in California's Central Valley, USA, seasonal and spatial controls on methylmercury (MeHg) production were examined in surface sediment. Three types of shallowly-flooded agricultural wetlands (white rice, wild rice, and fallow fields) and two types of managed (non-agricultural) wetlands (permanently and seasonally flooded) were sampled monthly-to-seasonally. Dynamic seasonal changes in readily reducible 'reactive' mercury (Hg(II)R), Hg(II)-methylation rate constants (kmeth), and concentrations of electron acceptors (sulfate and ferric iron) and donors (acetate), were all observed in response to field management hydrology, whereas seasonal changes in these parameters were more muted in non-agricultural managed wetlands. Agricultural wetlands exhibited higher sediment MeHg concentrations than did non-agricultural wetlands, particularly during the fall through late-winter (post-harvest) period. Both sulfate- and iron-reducing bacteria have been implicated in MeHg production, and both were demonstrably active in all wetlands studied. Stoichiometric calculations suggest that iron-reducing bacteria dominated carbon flow in agricultural wetlands during the growing season. Sulfate-reducing bacteria were not stimulated by the addition of sulfate-based fertilizer to agricultural wetlands during the growing season, suggesting that labile organic matter, rather than sulfate, limited their activity in these wetlands. Along the continuum of sediment geochemical conditions observed, values of kmeth increased approximately 10,000-fold, whereas Hg(II)R decreased 100-fold. This suggests that, with respect to the often opposing trends of Hg(II)-methylating microbial activity and Hg(II) availability for methylation, microbial activity dominated the Hg(II)-methylation process, and that along this biogeochemical continuum, conditions that favored microbial sulfate reduction resulted in the highest calculated MeHg production potential rates. Rice straw management options aimed at limiting labile carbon supplies to surface sediment during the post-harvest fall-winter period may be effective in limiting MeHg production within agricultural wetlands.

Biotechnological Production of Polyhydroxyalkanoates: A Review on Trends and Latest Developments

Polyhydroxyalkanoates (PHA) producers have been reported to reside at various ecological niches which are naturally or accidently exposed to high organic matter or growth limited conditions such as dairy wastes, hydrocarbon contaminated sites, pulp and paper mill wastes, agricultural wastes, activated sludges of treatment plants, rhizosphere, and industrial effluents. Few among them also produce extracellular by-products like rhamnolipids, extracellular polymeric substances, and biohydrogen gas. These sorts of microbes are industrially important candidates for the reason that they can use waste materials of different origin as substrate with simultaneous production of valuable bioproducts including PHA. Implementation of integrated system to separate their by-products (intracellular and extracellular) can be economical in regard to production. In this review, we have discussed various microorganisms dwelling at different environmental conditions which stimulate them to accumulate carbon as polyhydroxyalkanoates granules and factors influencing its production and composition. A brief aspect on metabolites which are produced concomitantly with PHA has also been discussed. In conclusion, exploring of capabilities like of dual production by microbes and use of wastes as renewable substrate under optimized cultural conditions either in batch or continuous process can cause deduction in present cost of bioplastic production from stored PHA granules.

Diversity of the bacterial community in the rice rhizosphere managed under conventional and no-tillage practices

Bacterial diversity in the rice rhizosphere at different rice growth stages, managed under conventional and no-tillage practices, was explored using a culture-based approach. Actinobacteria are among the bacterial phyla abundant in the rice rhizosphere. Their diversity was further examined by constructing metagenomic libraries based on the 16S rRNA gene, using actinobacterial- and streptomycete-specific polymerase chain reaction (PCR) primers. The study included 132 culturable strains and 125 clones from the 16S rRNA gene libraries. In conventional tillage, there were 38% Proteobacteria, 22% Actinobacteria, 33% Firmicutes, 5% Bacteroidetes, and 2% Acidobacteria, whereas with no-tillage management there were 63% Proteobacteria, 24% Actinobacteria, 6% Firmicutes, and 8% Bacteroidetes as estimated using the culture-dependent method during the four stages of rice cultivation. Principal coordinates analysis was used to cluster the bacterial communities along axes of maximal variance. The different growth stages of rice appeared to influence the rhizosphere bacterial profile for both cultivation practices. Novel clones with low similarities (89-97%) to Actinobacteria and Streptomyces were retrieved from both rice fields by screening the 16S rRNA gene libraries using actinobacterial- and streptomycete-specific primers. By comparing the actinobacterial community retrieved by culture-dependent and molecular methods, it was clear that a more comprehensive assessment of microbial diversity in the rice rhizosphere can be obtained using a combination of both techniques than by using either method alone. We also succeeded in culturing a number of bacteria that were previously described as unculturable. These were in a phylogenetically deep lineage when compared with related cultivable genera.

ACC deaminase and IAA producing growth promoting bacteria from the rhizosphere soil of tropical rice plants

Beneficial plant-associated bacteria play a key role in supporting and/or promoting plant growth and health. Plant growth promoting bacteria present in the rhizosphere of crop plants can directly affect plant metabolism or modulate phytohormone production or degradation. We isolated 355 bacteria from the rhizosphere of rice plants grown in the farmers' fields in the coastal rice field soil from five different locations of the Ganjam district of Odisha, India. Six bacteria producing both ACC deaminase (ranging from 603.94 to 1350.02 nmol α-ketobutyrate mg(-1)  h(-1) ) and indole acetic acid (IAA; ranging from 10.54 to 37.65 μM ml(-1) ) in pure cultures were further identified using polyphasic taxonomy including BIOLOG((R)) , FAME analysis and the 16S rRNA gene sequencing. Phylogenetic analyses of the isolates resulted into five major clusters to include members of the genera Bacillus, Microbacterium, Methylophaga, Agromyces, and Paenibacillus. Seed inoculation of rice (cv. Naveen) by the six individual PGPR isolates had a considerable impact on different growth parameters including root elongation that was positively correlated with ACC deaminase activity and IAA production. The cultures also had other plant growth attributes including ammonia production and at least two isolates produced siderophores. Study indicates that presence of diverse rhizobacteria with effective growth-promoting traits, in the rice rhizosphere, may be exploited for a sustainable crop management under field conditions.

Soil eukaryotic microorganism succession as affected by continuous cropping of peanut--pathogenic and beneficial fungi were selected

Peanut is an important oil crop worldwide and shows considerable adaptability but growth and yield are negatively affected by continuous cropping. Soil micro-organisms are efficient bio-indicators of soil quality and plant health and are critical to the sustainability of soil-based ecosystem function and to successful plant growth. In this study, 18S rRNA gene clone library analyses were employed to study the succession progress of soil eukaryotic micro-organisms under continuous peanut cultivation. Eight libraries were constructed for peanut over three continuous cropping cycles and its representative growth stages. Cluster analyses indicated that soil micro-eukaryotic assemblages obtained from the same peanut cropping cycle were similar, regardless of growth period. Six eukaryotic groups were found and fungi predominated in all libraries. The fungal populations showed significant dynamic change and overall diversity increased over time under continuous peanut cropping. The abundance and/or diversity of clones affiliated with Eurotiales, Hypocreales, Glomerales, Orbiliales, Mucorales and Tremellales showed an increasing trend with continuous cropping but clones affiliated with Agaricales, Cantharellales, Pezizales and Pyxidiophorales decreased in abundance and/or diversity over time. The current data, along with data from previous studies, demonstrated that the soil microbial community was affected by continuous cropping, in particular, the pathogenic and beneficial fungi that were positively selected over time, which is commonplace in agro-ecosystems. The trend towards an increase in fungal pathogens and simplification of the beneficial fungal community could be important factors contributing to the decline in peanut growth and yield over many years of continuous cropping.

Bacterial community analysis of the water surface layer from a rice-planted and an unplanted flooded field

The bacterial communities in floodwater, from a rice-planted and an unplanted field were characterized at the beginning (flooding stage) and at the end (harvest stage) of the rice cropping cycle. Most probable number estimations and plate counts of aerobic and anaerobic heterotrophic bacteria and of several metabolic bacterial groups (methanogens, sulfate-reducers, anaerobic sulfur and nonsulfur phototrophs, denitrifiers and ammonifiers) were similar in rice and unplanted floodwater at both sampling times. The analysis of denitrifiers and methanogens by fluorescent in situ hybridization revealed a shift in the phylogenetic affiliation only of the former group in the rice-planted floodwater. Terminal restriction fragment length polymorphism of 16S rRNA gene amplicons indicated that the bacterial communities of the rice-planted and unplanted soils were consistently diverse and strongly influenced by the season.

Nitrification-denitrification dynamics and community structure of ammonia oxidizing bacteria in a high yield irrigated Philippine rice field

Nitrogen is the single most limiting factor for rice production. Detailed knowledge on nitrogen dynamics in rice fields is therefore of major importance for developing sustainable rice production. A combination of state-of-the-art microsensor, stable isotope tracer, and molecular techniques was used to evaluate coupled nitrification-denitrification potentials and community structure of ammonia-oxidizing bacteria in a high yield irrigated rice cropping system in the Philippines, without the use of microcosm incubations. The multiple approaches showed a high degree of concordance among methods and thereby clarified the investigated processes. Numbers and potential activity of ammonia-oxidizing bacteria in the system reflected the availability of substrate in three defined soil factions with a ranking of: surface soil > rhizosphere > bulk soil. No nitrification activity was measured between spit applications of N fertilizer. However, nitrification was induced upon nitrogen amendment in intact soil cores. Despite induction by nitrogen amendment, the loss of nitrogen through coupled nitrification-denitrification was less than 10% of the plant nitrogen uptake. Denaturant gradient gel electrophoresis of amoA fragments revealed no differences in diversity profiles between the soil fractions, and phylogenetic analysis, based on amoA genes retrieved from the rice paddy soil, identified a set of mutually very similar sequences related to Nitrosomonas nitrosa.

Linking microbial community dynamics to rhizosphere carbon flow in a wetland rice soil

Photosynthesis by terrestrial vegetation is the driving force of carbon cycling between soil and the atmosphere. The soil microbiota, the decomposers of organic matter, is the second player carrying out carbon cycling. Numerous efforts have been made to quantify rhizodeposition and soil respiration to understand and predict the carbon cycling between the soil and atmosphere. However, there have been few attempts to link directly the soil microbial community to plant photosynthesis. We carried out a pulse-chase labeling experiment in a wetland rice system in which rice plants of various ages were labeled with (13)CO(2) for 6 h and the distribution of the assimilated (13)C to soil microorganisms was estimated by analyzing the (13)C profile of microbial phospholipid fatty acids (PLFAs). The results showed that total PLFA increased with plant growth, indicating an increase of microbial biomass. But the mono-unsaturated PLFAs increased faster than the branched chain fatty acids. The (13)C was incorporated into PLFAs immediately after the plant (13)CO(2) assimilation, proving the tight coupling of microbial activity to plant photosynthesis. In line with the finding of seasonal change in total PLFAs, more of (13)C was distributed to the straight chain fatty acids (16:0, 16:1omega7, 18:1omega7 and 18:1omega9) than to the branched chain fatty acids. The total plant carbon incorporation estimated from (13)C labeling roughly corresponded to the increase in total PLFAs over the growing season of plants. Our study suggests that microbial populations in rice soil differ greatly in their responses to plant photosynthate input.

The role of conservation agriculture in sustainable agriculture

The paper focuses on conservation agriculture (CA), defined as minimal soil disturbance (no-till, NT) and permanent soil cover (mulch) combined with rotations, as a more sustainable cultivation system for the future. Cultivation and tillage play an important role in agriculture. The benefits of tillage in agriculture are explored before introducing conservation tillage (CT), a practice that was borne out of the American dust bowl of the 1930s. The paper then describes the benefits of CA, a suggested improvement on CT, where NT, mulch and rotations significantly improve soil properties and other biotic factors. The paper concludes that CA is a more sustainable and environmentally friendly management system for cultivating crops. Case studies from the rice-wheat areas of the Indo-Gangetic Plains of South Asia and the irrigated maize-wheat systems of Northwest Mexico are used to describe how CA practices have been used in these two environments to raise production sustainably and profitably. Benefits in terms of greenhouse gas emissions and their effect on global warming are also discussed. The paper concludes that agriculture in the next decade will have to sustainably produce more food from less land through more efficient use of natural resources and with minimal impact on the environment in order to meet growing population demands. Promoting and adopting CA management systems can help meet this goal.

Traditional cattle manure application determines abundance, diversity and activity of methanogenic Archaea in arable European soil

Based on lipid analyses, 16S rRNA/rRNA gene single-strand conformation polymorphism fingerprints and methane flux measurements, influences of the fertilization regime on abundance and diversity of archaeal communities were investigated in soil samples from the long-term (103 years) field trial in Bad Lauchstädt, Germany. The investigated plots followed a gradient of increasing fertilization beginning at no fertilization and ending at the 'cattle manure' itself. The archaeal phospholipid etherlipid (PLEL) concentration was used as an indicator for archaeal biomass and increased with the gradient of increasing fertilization, whereby the concentrations determined for organically fertilized soils were well above previously reported values. Methane emission, although at a low level, were occasionally only observed in organically fertilized soils, whereas the other treatments showed significant methane uptake. Euryarchaeotal organisms were abundant in all investigated samples but 16S rRNA analysis also demonstrated the presence of Crenarchaeota in fertilized soils. Lowest molecular archaeal diversity was found in highest fertilized treatments. Archaea phylogenetically most closely related to cultured methanogens were abundant in these fertilized soils, whereas Archaea with low relatedness to cultured microorganisms dominated in non-fertilized soils. Relatives of Methanoculleus spp. were found almost exclusively in organically fertilized soils or cattle manure. Methanosarcina-related microorganisms were detected in all soils as well as in the cattle manure, but soils with highest organic application rate were specifically dominated by a close phylogenetic relative of Methanosarcina thermophila. Our findings suggest that regular application of cattle manure increased archaeal biomass, but reduced archaeal diversity and selected for methanogenic Methanoculleus and Methanosarcina strains, leading to the circumstance that high organic fertilized soils did not function as a methane sink at the investigated site anymore.

Determination of community structure through deconvolution of PLFA-FAME signature of mixed population

Phospholipid fatty acids (PLFAs) as biomarkers are well established in the literature. A general method based on least square approximation (LSA) was developed for the estimation of community structure from the PLFA signature of a mixed population where biomarker PLFA signatures of the component species were known. Fatty acid methyl ester (FAME) standards were used as species analogs and mixture of the standards as representative of the mixed population. The PLFA/FAME signatures were analyzed by gas chromatographic separation, followed by detection in flame ionization detector (GC-FID). The PLFAs in the signature were quantified as relative weight percent of the total PLFA. The PLFA signatures were analyzed by the models to predict community structure of the mixture. The LSA model results were compared with the existing "functional group" approach. Both successfully predicted community structure of mixed population containing completely unrelated species with uncommon PLFAs. For slightest intersection in PLFA signatures of component species, the LSA model produced better results. This was mainly due to inability of the "functional group" approach to distinguish the relative amounts of the common PLFA coming from more than one species. The performance of the LSA model was influenced by errors in the chromatographic analyses. Suppression (or enhancement) of a component's PLFA signature in chromatographic analysis of the mixture, led to underestimation (or overestimation) of the component's proportion in the mixture by the model. In mixtures of closely related species with common PLFAs, the errors in the common components were adjusted across the species by the model.

Distribution and density of bacteria in subtropical flooded rice growing areas in Brazil

Since microorganisms are important components in the structure and function of water systems, the present paper reports work done to identify groups making up bacterial communities present in rice irrigation water. To this end, water samples were collected in five rice-growing areas of Rio Grande do Sul State, Brazil. The identification of the main bacterial groups found in flooded areas was carried out based on colony morphology, taking into account shape, elevation, and edges. Internal and external cell structure was characterized as cocci or rod, gram-positive or gram-negative, and spore forming or not. The results obtained regarding density and bacterial distribution in the water samples from rice growing areas of RS showed a higher abundance of morphotypes of bacterial colonies in the irrigation channels (F1, 12 = 8.74; p < 0.05) when compared to the culture plots in the five production regions, and in the final culture phase (F1, 12 = 8.86; p < 0.05). In the five rice production areas the occurrence of gram-positive and spore-forming rods was prevalent. Rods showed more abundance (F1, 26 = 15.12; p < 0.05) in the early culture phase, with a significant prevalence of gram-positive rods (F1, 26 = 25.99; p < 0.05) in all rice growing regions under investigation. The group of spore-forming bacteria was significantly more abundant (F1, 30 = 14.06; p < 0.05) when compared with the non-spore-forming ones in all investigated regions. Data showed that the irrigated rice crop affects the density and morphotype colonies in the bacteria found in the water used to flood rice-growing plots.

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

Exploration of environmental factors governing soil microbial community composition is long overdue and now possible with improved methods for characterizing microbial communities. Previously, we observed that rice soil microbial communities were distinctly different from tomato soil microbial communities, despite management and seasonal variations within soil type. Potential contributing factors included types and amounts of organic inputs, organic carbon content, and timing and amounts of water inputs. Of these, both soil water content and organic carbon availability were highly correlated with observed differences in composition. We examined how organic carbon amendment (compost, vetch, or no amendment) and water additions (from air dry to flooded) affect microbial community composition. Using canonical correspondence analysis of phospholipid fatty acid data, we determined flooded, carbon-amended (+C) microcosm samples were distinctly different from other +C samples and unamended (-C) samples. Although flooding without organic carbon addition influenced composition some, organic carbon addition was necessary to substantially alter community composition. Organic carbon availability had the same general effects on microbial communities regardless of whether it was compost or vetch in origin. In addition, flooded samples, regardless of organic carbon inputs, had significantly lower ratios of fungal to bacterial biomarkers, whereas under drier conditions and increased organic carbon availability the microbial communities had higher proportions of fungal biomass. When comparing field and microcosm soil, flooded +C microcosm samples were most similar to field-collected rice soil, whereas all other treatments were more similar to field-collected tomato soil. Overall, manipulating water and carbon content selected for microbial communities similar to those observed when the same factors were manipulated at the field scale.

Comparison of signature lipid methods to determine microbial community structure in compost

The microbial community structure changes substantially during the composting process and simple methods to follow these changes can potentially be used to estimate compost maturity. In this study, two such methods, the microbial identification (MIDI) method and the ester-linked (EL) procedure to determine the composition of long-chain fatty acids, were applied to compost samples of different age. The ability of the two methods to describe the microbial succession was evaluated by comparison with phospholipid fatty acid (PLFA) analysis on the same samples.Samples were taken from a 200-l laboratory compost reactor, treating source-separated organic household waste. During the initial stages of the process, the total concentration of fatty acids in compost samples treated with the EL and MIDI methods was many times higher than with the PLFA method. This was probably due to the presence of fatty acids from the organic material in the original waste. However, this substantial difference between PLFA and the other two methods was not found later in composting. Although the PLFA method gave the most detailed information about the growth and overall succession of the microbial community, the much simpler MIDI and EL methods also successfully described the shift from the initially dominating straight chain fatty acids to iso- and anteiso branched, 10 Me branched and cyclopropane fatty acids in the later stages of the process. Thus, the MIDI and EL extraction methods appear to be suitable for analysis of microbial FAME profiles in compost, particularly in the later stages of the process.

Isolation and Molecular Characterization of Thiosulfate-oxidizing Bacteria from an Italian Rice Field Soil

In rice paddy soils an active cycling of sulfur compounds takes place. To elucidate the diversity of thiosulfate-oxidizing bacteria these organisms were enriched from bulk soil and rice roots by the most probable number method in liquid medium. From the MPN enrichment cultures 21 bacterial strains were isolated on solid mineral medium, and could be further shown to produce sulfate from thiosulfate. These strains were characterized by 16S rDNA analyses. The isolates were affiliated to seven different phylogenetic groups within the alpha- and beta-subclass of Proteobacteria. Two of these phylotypes were already described as S-oxidizers in this environment (Xanthobacter sp. and Bosea sp. related strains), but five groups represented new S-oxidizers in rice field soil. These isolates were closely related to Mesorhizobium loti, to Hydrogenophaga sp., to Delftia sp., to Pandoraea sp. or showed sequence similarity to a strain of Achromobacter sp.

Enumeration of 16S rDNA of Desulfotomaculum lineage 1 in rice field soil by real-time PCR with SybrGreen detection

Real-time PCR is a new and highly sensitive method for the quantification of microbial organisms in environmental samples. This work was conducted to evaluate real-time PCR with SybrGreen (SG) detection as quantification method for Desulfotomaculum lineage 1 organisms in samples of rice field soil. The method was optimized in several parameters like SG concentration. These allowed quantitative PCR with different primer combinations yielding PCR products with lengths up to 1066 bp and with sensitivities of 10(2) targets for all assays. The detection limit in environmental DNA extracts (rice bulk soil and rice roots) was 10(6) targets per gram dry weight according to the dilution of the DNA extracts necessary to overcome PCR inhibition of humic substances. A verification, that the fluorescence increase was due to specific PCR products, was done by agarose gel electrophoresis since melting curve analysis of the PCR products did not show a distinct peak in the first derivative, when the environmental DNA extracts were used in PCR. Amplification with a primer combination specific for Desulfotomaculum lineage 1 organisms showed an abundance of this group of approximately 2% and 0.5% of the eubacterial 16S rDNA targets in rice bulk soil and rice root samples, respectively. Approximately half of this number was obtained in both habitats with a PCR assay specific for a Desulfotomaculum sequence cluster obtained previously from rice field soil.

Population dynamics of type I and II methanotrophic bacteria in rice soils

Methane-oxidizing bacteria (methanotrophs) consume a significant but variable fraction of greenhouse-active methane gas produced in wetlands and rice paddies before it can be emitted to the atmosphere. Temporal and spatial dynamics of methanotroph populations in California rice paddies were quantified using phospholipid biomarker analyses in order to evaluate the relative importance of type I and type II methanotrophs with depth and in relation to rice roots. Methanotroph population fluctuations occurred primarily within the top 0-2 cm of soil, where methanotroph cells increased by a factor of 3-5 over the flooded rice-growing season. The results indicate that rice roots and rhizospheres were less important than the soil-water interface in supporting methanotroph growth. Both type I and type II methanotrophs were abundant throughout the year. However, only type II populations were strongly correlated with soil porewater methane concentrations and rice growth.

Thermophilic methanogens in rice field soil

The soil temperature in flooded Italian rice fields is generally lower than 30 degrees C. However, two temperature optima at approximately 41 degrees C and 50 degrees C were found when soil slurries were anoxically incubated at a temperature range of 10-80 degrees C. The second temperature optimum indicates the presence of thermophilic methanogens in the rice field soil. Experiments with 14C-labelled bicarbonate showed that the thermophilic CH4 was exclusively produced from H2/CO2. Terminal restriction fragment length polymorphism (T-RFLP) of archaeal SSU rRNA gene fragments revealed a dramatic change in the archaeal community structure at temperatures > 37 degrees C, with the euryarchaeotal rice cluster I becoming the dominant group (about 80%). A clone library of archaeal SSU rRNA gene fragments generated at 49 degrees C was also dominated (10 out of 11 clones) by rice cluster I. Our results demonstrate that Italian rice field soil contains thermophilic methanogenic activity that was most probably a result of members of the as yet uncultivated euryarchaeotal rice cluster I.

Bacterial populations colonizing and degrading rice straw in anoxic paddy soil

Rice straw is a major substrate for the production of methane, a greenhouse gas, in flooded rice fields. The bacterial community degrading rice straw under anoxic conditions was investigated with molecular methods. Rice straw was incubated in paddy soil anaerobically for 71 days. Denaturing gradient gel electrophoresis (DGGE) of the amplified bacterial 16S rRNA genes showed that the composition of the bacterial community changed during the first 15 days but then was stable until the end of incubation. Fifteen DGGE bands with different signal intensities were excised, cloned, and sequenced. In addition, DNA was extracted from straw incubated for 1 and 29 days and the bacterial 16S rRNA genes were amplified and cloned. From these clone libraries 16 clones with different electrophoretic mobilities on a DGGE gel were sequenced. From a total of 31 clones, 20 belonged to different phylogenetic clusters of the clostridia, i.e., clostridial clusters I (14 clones), III (1 clone), IV (1 clone), and XIVa (4 clones). One clone fell also within the clostridia but could not be affiliated to one of the clostridial clusters. Ten clones grouped closely with the genera Bacillus (3 clones), Nitrosospira (1 clone), Fluoribacter (1 clones), and Acidobacterium (2 clones) and with clone sequences previously obtained from rice field soil (3 clones). The relative abundances of various phylogenetic groups in the rice straw-colonizing community were determined by fluorescence in situ hybridization (FISH). Bacteria were detached from the incubated rice straw with an efficiency of about 80 to 90%, as determined by dot blot hybridization of 16S rRNA in extract and residue. The number of active (i.e., a sufficient number of ribosomes) Bacteria detected with a general eubacterial probe (Eub338) after 8 days of incubation was 61% of the total cell counts. This percentage decreased to 17% after 29 days of incubation. Most (55%) of the active cells on day 8 belonged to the genus Clostridium, mainly to clostridial clusters I (24%), III (6%), and XIVa (24%). An additional 5% belonged to the Cytophaga-Flavobacterium cluster of the Cytophaga-Flavobacterium-Bacteroides phylum, 4% belonged to the alpha, beta, and gamma Proteobacteria, and 1.3% belonged to the Bacillus subbranch of the gram-positive bacteria with a low G+C content. The results show that the bacterial community colonizing and decomposing rice straw developed during the first 15 days of incubation and was dominated by members of different clostridial clusters, especially clusters I, III, and XIVa.

Effect of temperature on carbon and electron flow and on the archaeal community in methanogenic rice field soil

Temperature is an important factor controlling CH(4) production in anoxic rice soils. Soil slurries, prepared from Italian rice field soil, were incubated anaerobically in the dark at six temperatures of between 10 to 37 degrees C or in a temperature gradient block covering the same temperature range at intervals of 1 degrees C. Methane production reached quasi-steady state after 60 to 90 days. Steady-state CH(4) production rates increased with temperature, with an apparent activation energy of 61 kJ mol(-1). Steady-state partial pressures of the methanogenic precursor H(2) also increased with increasing temperature from <0.5 to 3.5 Pa, so that the Gibbs free energy change of H(2) plus CO(2)-dependent methanogenesis was kept at -20 to -25 kJ mol of CH(4)(-1) over the whole temperature range. Steady-state concentrations of the methanogenic precursor acetate, on the other hand, increased with decreasing temperature from <5 to 50 microM. Simultaneously, the relative contribution of H(2) as methanogenic precursor decreased, as determined by the conversion of radioactive bicarbonate to (14)CH(4), so that the carbon and electron flow to CH(4) was increasingly dominated by acetate, indicating that psychrotolerant homoacetogenesis was important. The relative composition of the archaeal community was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes (16S rDNA). T-RFLP analysis differentiated the archaeal Methanobacteriaceae, Methanomicrobiaceae, Methanosaetaceae, Methanosarcinaceae, and Rice clusters I, III, IV, V, and VI, which were all present in the rice field soil incubated at different temperatures. The 16S rRNA genes of Rice cluster I and Methanosaetaceae were the most frequent methanogenic groups. The relative abundance of Rice cluster I decreased with temperature. The substrates used by this microbial cluster, and thus its function in the microbial community, are unknown. The relative abundance of acetoclastic methanogens, on the other hand, was consistent with their physiology and the acetate concentrations observed at the different temperatures, i.e., the high-acetate-requiring Methanosarcinaceae decreased and the more modest Methanosaetaceae increased with increasing temperature. Our results demonstrate that temperature not only affected the activity but also changed the structure and the function (carbon and electron flow) of a complex methanogenic system.

Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms

Because excised, washed roots of rice (Oryza sativa) immediately produce CH4 when they are incubated under anoxic conditions (P. Frenzel and U. Bosse, FEMS Microbiol. Ecol. 21:25-36, 1996), we employed a culture-independent molecular approach to identify the methanogenic microbial community present on roots of rice plants. Archaeal small-subunit rRNA-encoding genes were amplified directly from total root DNA by PCR and then cloned. Thirty-two archaeal rice root (ARR) gene clones were randomly selected, and the amplified primary structures of ca. 750 nucleotide sequence positions were compared. Only 10 of the environmental sequences were affiliated with known methanogens; 5 were affiliated with Methanosarcina spp., and 5 were affiliated with Methanobacterium spp. The remaining 22 ARR gene clones formed four distinct lineages (rice clusters I through IV) which were not closely related to any known cultured member of the Archaea. Rice clusters I and II formed distinct clades within the phylogenetic radiation of the orders "Methanosarcinales" and Methanomicrobiales. Rice cluster I was novel, and rice cluster II was closely affiliated with environmental sequences obtained from bog peat in northern England. Rice cluster III occurred on the same branch as Thermoplasma acidophilum and marine group II but was only distantly related to these taxa. Rice cluster IV was a deep-branching crenarchaeotal assemblage that was closely related to clone pGrfC26, an environmental sequence recovered from a temperate marsh environment. The use of a domain-specific oligonucleotide probe in a fluorescent in situ hybridization analysis revealed that viable members of the Archaea were present on the surfaces of rice roots. In addition, we describe a novel euryarchaeotal main line of descent, designated rice cluster V, which was detected in anoxic rice paddy soil. These results indicate that there is an astonishing richness of archaeal diversity present on rice roots and in the surrounding paddy soil.

Sulfur oxidation in rice field soil: activity, enumeration, isolation and characterization of thiosulfate-oxidizing bacteria

In rice paddy fields the bulk soil is anoxic, but oxygenated zones occur in the surrounding of the rice roots to where oxygen is transported via the aerenchyma system of the rice plants. In the anaerobic soil compartments sulfate is consumed by sulfate-reducing bacteria. In the rhizosphere the reduced sulfur compounds can be reoxidized by sulfur-oxidizing bacteria. Measurements of the potential activity of thiosulfate-oxidizing bacteria in soil slurries derived from planted rice soil microcosms showed turnover rates of 2-6 mumol d-1 g-dw-1. Thiosulfate was oxidized to sulfate with tetrathionate as intermediate. Most probable number (MPN) enumeration with three aerobic media and one anaerobic nitrate-amended medium showed that thiosulfate-oxidizing bacteria were abundant in paddy soil and in rhizosphere soil at numbers of 10(5) to 10(6) per gram dry weight soil. Nine isolates of S-oxidizing bacteria were obtained from enrichment cultures or from the highest dilutions of the MPN series and were affiliated to four different phylogenetic groups. These isolates were characterized by physiological properties and by comparative 16S rDNA sequence analysis. Three isolates (TA1-AE1, TA1-A1 and TA12-21) were shown to be facultatively chemolithoautotrophic strains of Ancylobacter aquaticus. Three further isolates (Tv6-2b, Z2A-6A and Z4A-2A) were also facultatively chemolithoautotrophic and were affiliated with the Xanthobacter sp. group, probably representing new strains of X. flavus or X. tagetidis. Strain SZ-2111 was phylogenetically related to Bosea thiooxidans. However, the genus Bosea is described as obligately heterotrophic, whereas strain 5Z-2111 was able to grow autotrophically. The isolates 5Z-C1 and TBW3 were obligate chemolithoautotrophs and were closely affiliated with Thiobacillus thioparus. Our results showed that S-oxidizing bacteria were abundant and active in rice paddy soil and consisted of physiologically and phylogenetically diverse populations.

Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval

A dual approach consisting of cultivation and molecular retrieval of partial archaeal 16S rRNA genes was carried out to characterize the diversity and structure of the methanogenic community inhabiting the anoxic bulk soil of flooded rice microcosms. The molecular approach identified four groups of known methanogens. Three environmental sequences clustered with Methanobacterium bryantii and Methanobacterium formicicum, six were closely related but not identical to those of strains of Methanosaeta concilii, two grouped with members of the genus Methanosarcina, and two were related to the methanogenic endosymbiont of Plagiopyla nasuta. The cultivation approach via most-probable-number counts with a subsample of the same soil as an inoculum yielded cell numbers of up to 10(7) per g of dry soil for the H2-CO2-utilizing methanogens and of up to 10(6) for the acetate-utilizing methanogens. Strain VeH52, isolated from the terminal positive dilution on H2-CO2, grouped within the phylogenetic radiation characterized by M. bryantii and M. formicicum and the environmental sequences of the Methanobacterium-like group. A consortium of two distinct methanogens grew in the terminal positive culture on acetate. These two organisms showed absolute 16S rRNA gene identities with environmental sequences of the novel Methanosaeta-like group and the Methanobacterium-like group. Methanosarcina spp. were identified only in the less-dilute levels of the same dilution series on acetate. These data correlate well with acetate concentrations of about 11 microM in the pore water of this rice paddy soil. These concentrations are too low for the growth of known Methanosarcina spp. but are at the acetate utilization threshold of Methanosaeta spp. Thus, our data indicated Methanosaeta spp. and Methanobacterium spp. to be the dominant methanogenic groups in the anoxic rice soil, whereas Methanosarcina spp. appeared to be less abundant.

Distribution of a Population of Rhizobium leguminosarum bv. trifolii among Different Size Classes of Soil Aggregates

A combination of the plant infection-soil dilution technique (most-probable-number [MPN] technique) and immunofluorescence direct count (IFDC) microscopy was used to examine the effects of three winter cover crop treatments on the distribution of a soil population of Rhizobium leguminosarum bv. trifolii across different size classes of soil aggregates (<0.25, 0.25 to 0.5, 0.5 to 1.0, 1.0 to 2.0, and 2.0 to 5.0 mm). The aggregates were prepared from a Willamette silt loam soil immediately after harvest of broccoli (September 1995) and before planting and after harvest of sweet corn (June and September 1996, respectively). The summer crops were grown in soil that had been either fallowed or planted with a cover crop of red clover (legume) or triticale (cereal) from September to April. The Rhizobium soil population was heterogeneously distributed across the different size classes of soil aggregates, and the distribution was influenced by cover crop treatment and sampling time. On both September samplings, the smallest size class of aggregates (<0.25 mm) recovered from the red clover plots carried between 30 and 70% of the total nodulating R. leguminosarum population, as estimated by the MPN procedure, while the same aggregate size class from the June sampling carried only ∼6% of the population. In June, IDFC microscopy revealed that the 1.0- to 2.0-mm size class of aggregates from the red clover treatment carried a significantly greater population density of the successful nodule-occupying serotype, AR18, than did the aggregate size classes of <0.5 mm, and 2 to 5 mm. In September, however, the population profile of AR18 had shifted such that the density was significantly greater in the 0.25- to 0.5-mm size class than in aggregates of <0.25 mm and >1.0 mm. The populations of two other Rhizobium serotypes (AR6 and AS36) followed the same trends of distribution in the June and September samplings. These data indicate the existence of structural microsites that vary in their suitabilities to support growth and protection of bacteria and that are influenced by the presence and type of plant grown in the soil.