Use of phospholipid fatty acids and carbon source utilization patterns To track microbial community succession in developing compost

Lytic polysaccharide monooxygenases (LPMOs) producing microbes: A novel approach for rapid recycling of agricultural wastes

Out of the huge quantity of agricultural wastes produced globally, rice straw is one of the most abundant ligno-cellulosic waste. For efficient utilization of these wastes, several cost-effective biological processes are available. The practice of field level in-situ or ex-situ decomposition of rice straw is having less degree of adoption due to its poor decomposition ability within a short time span between rice harvest and sowing of the next crop. Agricultural wastes including rice straw are in general utilized by using lignocellulose degrading microbes for industrial metabolite or compost production. However, bioconversion of crystalline cellulose and lignin present in the waste, into simple molecules is a challenging task. To resolve this issue, researchers have identified a novel new generation microbial enzyme i.e., lytic polysaccharide monooxygenases (LPMOs) and reported that the combination of LPMOs with other glycolytic enzymes are found efficient. This review explains the progress made in LPMOs and their role in lignocellulose bioconversion and the possibility of exploring LPMOs producers for rapid decomposition of agricultural wastes. Also, it provides insights to identify the knowledge gaps in improving the potential of the existing ligno-cellulolytic microbial consortium for efficient utilization of agricultural wastes at industrial and field levels.

Effects of different patterns of maize-straw application on soil microorganisms, enzyme activities, and grain yield

The present study aimed to assess the influences of corn straw application on the soil microbial organisms, soil enzyme activities and the grain yield. Four treatments were evaluated: (i) The straw was ploughed into soil using a fence hydraulic turning plow with ploughing depth of 30-40 cm(PD). (ii) The self-developed straw deep returning machine was used to bury 30-40 cm in the sub-surface layer of soil (SD). (iii) The straw was mulched and no tillage sowing(M). (iv)Without straw application(CK). Soil samples of different deep(0-20 cm, 20-40 cm soil layer) were taken during the corn growth stage to determinesoil biological characteristics.Our results suggested that soil microorganisms were not increased by straw mulching. Straw deep ploughing and returning (PD treatment) could effectively improve the phospholipid fatty acids(PLFAs) of bacteria, actinomycetes, and fungi, the activities of urease,invertase,dehydrogenase and polyphenoloxidase, even the grain yield. In 20-40 cm subsoil layer, the effects were more obvious than those of topsoil. The mean yield of PD treatment was higher than SD,M and CK. The results showed that the PLFA signatures and soil enzyme were both sensitive to the changes of soil environment condition by the application of straw. In the actual field production, we should adopt the appropriate way of straw returning to the field to achieve not only the improvement of soil quality, but also the increase of grain yield.

Changes in global trends in food waste composting: Research challenges and opportunities

Increasing food waste (FW) generation has put significant pressure on the environment and has increased the global financial costs of its appropriate management. Among the traditional organic waste recycling technologies (i.e., incineration, landfilling and anaerobic digestion), composting is an economically feasible and reliable technology for FW recycling regardless of its technical flaws and social issues. The global scenario of FW generation, technical advancement in FW composting and essential nutrient recovery from organic waste with waste recycling are discussed in this article. Recent research on various strategies to improve FW composting, including co-composting, the addition of organic/inorganic additives, the mitigation of gaseous emission, and microbiological variations are comprehensively explained. Subsequently, it is shown that the performing FW composting in an existing mechanical facility can improve organic waste degradation and produce value-added mature compost to save on costs and increase the technological feasibility and viability of FW composting to some extent.

Improvement of biochar and bacterial powder addition on gaseous emission and bacterial community in pig manure compost

Effect of bamboo biochar (BC) combined with two bacterial powders (B) on gaseous emission and variety of bacterial community during pig manure (PM) composting was investigated. The results showed that treatments of BC, BC + B1 and BC + B2 can reduce peak gaseous emission by 54%, 80% and 69% for CH₄, respectively, while 37%, 45% and 45% for N₂O, respectively, and 13%, 19% and 26% for NH₃, respectively. The evolution of the bacterial community quantified with 16S rDNA analysis showed that in the thermophile stage, total relative abundance percentage of bacterial phyla of Firmicutes and Proteobacteria reached 97%, 97%, 93% and 96% for CK, BC, BC + B1 and BC + B2, respectively. Effects of BC on the compost bacterial community variation analysis proved bacterial activity in the thermophile stage was controlled by the content of dissolved organic carbon and temperature of the compost mixture, while electrical conductivity and total kjeldahl nitrogen also influenced compost maturity stage.

Composting of food wastes: Status and challenges

This review analyses the main challenges of the process of food waste composting and examines the crucial aspects related to the quality of the produced compost. Although recent advances have been made in crucial aspects of the process, such composting microbiology, improvements are needed in process monitoring. Therefore, specific problems related to food waste composting, such as the presence of impurities, are thoroughly analysed in this study. In addition, environmental impacts related to food waste composting, such as emissions of greenhouse gases and odours, are discussed. Finally, the use of food waste compost in soil bioremediation is discussed in detail.

Comparison of characterization and microbial communities in rice straw- and wheat straw-based compost for Agaricus bisporus production

Rice straw (RS) is an important raw material for the preparation of Agaricus bisporus compost in China. In this study, the characterization of composting process from RS and wheat straw (WS) was compared for mushroom production. The results showed that the temperature in RS compost increased rapidly compared with WS compost, and the carbon (C)/nitrogen (N) ratio decreased quickly. The microbial changes during the Phase I and Phase II composting process were monitored using denaturing gradient gel electrophoresis (DGGE) and phospholipid fatty acid (PLFA) analysis. Bacteria were the dominant species during the process of composting and the bacterial community structure dramatically changed during heap composting according to the DGGE results. The bacterial community diversity of RS compost was abundant compared with WS compost at stages 4-5, but no distinct difference was observed after the controlled tunnel Phase II process. The total amount of PLFAs of RS compost, as an indicator of microbial biomass, was higher than that of WS. Clustering by DGGE and principal component analysis of the PLFA compositions revealed that there were differences in both the microbial population and community structure between RS- and WS-based composts. Our data indicated that composting of RS resulted in improved degradation and assimilation of breakdown products by A. bisporus, and suggested that the RS compost was effective for sustaining A. bisporus mushroom growth as well as conventional WS compost.

Manipulating soil microbial communities in extensive green roof substrates

There has been very little investigation into the soil microbial community on green roofs, yet this below ground habitat is vital for ecosystem functioning. Green roofs are often harsh environments that would greatly benefit from having a healthy microbial system, allowing efficient nutrient cycling and a degree of drought tolerance in dry summer months. To test if green roof microbial communities could be manipulated, we added mycorrhizal fungi and a microbial mixture ('compost tea') to green roof rootzones, composed mainly of crushed brick or crushed concrete. The study revealed that growing media type and depth play a vital role in the microbial ecology of green roofs. There are complex relationships between depth and type of substrate and the biomass of different microbial groups, with no clear pattern being observed. Following the addition of inoculants, bacterial groups tended to increase in biomass in shallower substrates, whereas fungal biomass change was dependent on depth and type of substrate. Increased fungal biomass was found in shallow plots containing more crushed concrete and deeper plots containing more crushed brick where compost tea (a live mixture of beneficial bacteria) was added, perhaps due to the presence of helper bacteria for arbuscular mycorrhizal fungi (AMF). Often there was not an additive affect of the microbial inoculations but instead an antagonistic interaction between the added AM fungi and the compost tea. This suggests that some species of microbes may not be compatible with others, as competition for limited resources occurs within the various substrates. The overall results suggest that microbial inoculations of green roof habitats are sustainable. They need only be done once for increased biomass to be found in subsequent years, indicating that this is a novel and viable method of enhancing roof community composition.

Investigating microbial activities during a starch-amended co-composting process at mesophilic and thermophilic temperatures

The aim of this study was to assess the use of functional microbial ecological techniques in detailing processes during composting. Using starch as an amendment for a co-composting process, small-scale individual mesocosms were investigated at two temperatures, 30 degrees C and 60 degrees C, over a five-week period. In order to determine the more exact processes occurring during degradation, extracellular enzyme analysis (EEA) and community-level physiological profiling (CLPP) were used. The EEA demonstrated that, although assay temperature effects were present, no significant difference between the two in situ composting temperatures was observed for the two enzyme substrates, alpha- and beta-glucosidase, used. The CLPP profiling was only performed on the 30 degrees C compost samples. These analyses indicated a dynamic, but broadly predictable, environment, suggesting that the use of this approach may be further applicable to these types of study. By investigating both total dry and organic weights, no difference in organic matter degradation between the two temperatures was observed. These results showed that either starch degradation acted independently of temperature or compensatory effects occurred. The former hypothesis was supported by a second experiment investigating starch degradation at both temperatures with appropriate negative controls. Trying to reconcile the EEA results with the changes in total matter was difficult without making speculative assumptions. The study highlights the need to further develop and evaluate these microbial ecological techniques to address such problems.

Functional changes in culturable microbial communities during a co-composting process: carbon source utilization and co-metabolism

Microbial communities in sewage sludge and green waste co-composting were investigated using culture-dependent methods and community level physiological profiles (CLPP) with Biolog Microplate. Different microbial groups characterized each stage of composting. Bacterial densities were high from beginning to end of composting, whereas actinomycete densities increased only after bio-oxidation phase i.e. after 40days. Fungal populations become particularly high during the last stage of decomposition. Cluster analyses of metabolic profiles revealed a similar separation between two groups of composts at 67days for bacteria and fungi. Principal component analysis (PCA) applied to bacterial and fungal CLPP data showed a chronological distribution of composts with two phases. The first one (before 67days), where the composts were characterized by the rapid decomposition of non-humic biodegradable organic matter, was significantly correlated to the decrease of C, C/N, organic matter (OM), fulvic acid (FA), respiration, cellulase, protease, phenoloxidase, alkaline and acid phosphatases activities. The second phase corresponding to the formation of polycondensed humic-like substances was significantly correlated to humic acid (HA) content, pH and HA/FA. The influent substrates selected on both factorial maps showed that microbial communities could adapt their metabolic capacities to the particular environment. The first phase seems to be focused on easily degradable substrate utilization whereas the maturation phase appears as multiple metabolisms, which induce the release of metabolites and their polymerization leading to humification processes.

Evaluation of in situ functional activity of casing soils during growth cycle of mushroom (Agaricus bisporus (Lange) Imbach) employing community level physiological profiles (CLPPs)

Community level physiological profiles (CLPPs) have been rarely applied to mushroom compost ecosystem, probably for the lack of standardized methodology. Recently, however CLPPs have been employed as a tool to investigate the degree of maturity of compost (Mondini and Insam, 2005, Compost Science and Utilization, 13(1): 27-33). The potential of CLPPs to detect compost maturity test is considerably significant in that it provides sensitivity and the simplicity of the assay. The aim of this work was to investigate the maturity of casing that comprised of farm yard manure and spent compost and influence of casing type on the behaviour of bacterial community during the growth cycle of mushroom Agaricus bisporus (Lange) Imbach employing standardized inoculum density and effects of different data interpretation based on the kinetics of colour formation. Casing samples of different age were extracted at a particular dilution and then inoculated in 96 well microtitre plates. Optical density (OD) in well was measured at 590 nm every 24 hours for 5 days. Principal component analysis (PCA) was performed by employing OD values at fixed average well colour development (AWCD). PCA of fresh samples showed that classification and ordination of samples according to their age were significant with fixed AWCD.

Microbial community structure and function during abnormal curve development of substrate-induced respiration measurements

Soil respiration measurements are an established method to test the abundance, activity and vitality of the soil microorganisms. However, abnormal progressions of soil respiration curves impede a clear interpretation of the data. The aim of this study was to investigate the changes in the microbial structure during the formation of phenomena like double peaks and terraces by analysis of the PLFA composition (phospholipid fatty acid composition). Moreover, 13C labeled glucose was used as substrate; therefore it was possible to measure delta13C values both within the PLFA fraction as well as within the carbon dioxide evolved during respiration. As contaminants trinitrotoluene, cycloheximide, and hexadecane were used. The results showed that the appearance of double peaks was mainly related to the growth of fungi with the marker 18:2delta9,12 due to a toxic effect of trinitrotoluene and cycloheximide. In contrast, the phenomenon of terrace formation was related to the utilization of hexadecane as a carbon source mainly by bacteria.

DGGE and T-RFLP analysis of bacterial succession during mushroom compost production and sequence-aided T-RFLP profile of mature compost

The amount of button mushroom (Agaricus bisporus) harvested from compost is largely affected by the microbial processes taking place during composting and the microbes inhabiting the mature compost. In this study, the microbial changes during the stages of this specific composting process were monitored, and the dominant bacteria of the mature compost were identified to reveal the microbiological background of the favorable properties of the heat-treated phase II mushroom compost. 16S ribosomal deoxyribonucleic acid (rDNA)-based denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) molecular fingerprinting methods were used to track the succession of microbial communities in summer and winter composting cycles. DNA from individual DGGE bands were reamplified and subjected to sequence analysis. Principal component analysis of fingerprints of the composting processes showed intensive changes in bacterial community during the 22-day procedure. Peak temperature samples grouped together and were dominated by Thermus thermophilus. Mature compost patterns were almost identical by both methods (DGGE, T-RFLP). To get an in-depth analysis of the mature compost bacterial community, the sequence data from cultivation of the bacteria and cloning of environmental 16S rDNA were uniquely coupled with the output of the environmental T-RFLP fingerprints (sequence-aided T-RFLP). This method revealed the dominance of a supposedly cellulose-degrading consortium composed of phylotypes related to Pseudoxanthomonas, Thermobifida, and Thermomonospora.

Analysis of bacterial activity, biomass and diversity during windrow composting

Two contrasting compost windrows were monitored for various physical, chemical and microbiological parameters for a period of 106 days. The different input materials and management practises gave rise to different temperature, moisture, and oxygen consumption profiles as composting proceeded. However, despite the different composting conditions, the specific respiratory activity, as determined by oxygen consumption per bacterial cell, was remarkably similar for both windrows. Further investigations into diversity dynamics were done through DGGE and cloning and sequencing of bacterial 16S rDNA PCR products. Although sequence analysis showed differing bacterial communities across time and between the different windrows, similarities in the progression were noted. The majority of sequences recovered from the first sampling period (day 1) were highly similar to previously isolated organisms. The clone libraries from the last sampling period (day 106) contained organisms that showed lower homology to their closest relatives, often with other uncultured organisms, and in phyla that contain few cultured representatives. These data suggest that specific respiratory activity may be an important driver of bacterial diversity in composting environments.

Microbial community dynamics during composting of sewage sludge and straw studied through phospholipid and neutral lipid analysis

The composting process involves a succession of different communities of microorganisms that decompose the initial material, transforming it into a stable final product. In this work, the levels of phospholipid fatty acid (PLFA), neutral lipid fatty acid (NLFA) and sterol were monitored in compost versus time, as indicators of the activity of various microorganisms (Gram-positive or Gram-negative bacteria, fungi, etc.). During composting, the PLFA and NLFA from Gram-negative bacteria and eukaryotes (2-OH 10; 3-OH 12; 2-OH 14; 13:0; 16:1; 18:1 trans) as well as some sterols of plant origin (e.g. monostearin sterols) decreased until the end of composting. In contrast, the branched fatty acids with iso- and anteiso-forms (i-15:0; a-15:0; i-16; i-17) increased mainly in the thermophilic phase, but decreased right after. The PLFA 18:2 (6; 9), which is used as an index of the occurrence of some fungi, rose strongly at the beginning of composting, but fell after peak heating. In contrast, the other main sterol indicative of fungi, ergosterol, decreased at the beginning of the thermophilic phase, but increased strongly by the end of composting. Accordingly, cluster and PCA analysis separated the PLFA of Gram-negative bacteria and eukaryotic cells from those of Gram-positive bacteria and long-chain fatty acids. The fungal PLFA considered, 18:2 (9, 12), was clustered more closely to iso- and anteiso-branched PLFAs. Stigmasterol, squalene and cholesterol occurred in the lower right part of the loading plot and were clustered more closely to iso-, anteiso-branched PLFAs and 18:2 w 6,9 suggesting their relationship to microbial activities. We also observed the tendency of resistance of fatty acid PLFAs and NLFAs of long chain (19:0 (cis-9); 20:0) and some recalcitrant sterols, e.g. sitosterol, at the end of composting. The presence of high levels of the latter in the final stage indicates their contribution to the structural stability of organic matter fractions. These recalcitrant components were more clustered and occurred in the lower right part of the loading plot.

Molecular microbial and chemical investigation of the bioremediation of two-phase olive mill waste using laboratory-scale bioreactors

Two-phase olive mill waste (TPOMW) is a semisolid effluent that is rich in contaminating polyphenols and is produced in large amounts by the industry of olive oil production. Laboratory-scale bioreactors were used to investigate the biodegradation of TPOMW by its indigenous microbiota. The effect of nutrient addition (inorganic N and P) and aeration of the bioreactors was studied. Microbial changes were investigated by PCR-temperature time gradient electrophoresis (TTGE) and following the dynamics of polar lipid fatty acids (PLFA). The greatest decrease in the polyphenolic and organic matter contents of bioreactors was concomitant with an increase in the PLFA fungal/bacterial ratio. Amplicon sequences of nuclear ribosomal internal transcribed spacer region (ITS) and 16S rDNA allowed identification of fungal and bacterial types, respectively, by comparative DNA sequence analyses. Predominant fungi identified included members of the genera Penicillium, Candida, Geotrichum, Pichia, Cladosporium, and Aschochyta. A total of 14 bacterial genera were detected, with a dominance of organisms that have previously been associated with plant material. Overall, this work highlights that indigenous microbiota within the bioreactors through stimulation of the fungal fraction, is able to degrade the polyphenolic content without the inoculation of specific microorganisms.

Use of Fatty Acid Methyl Ester Profiles to Compare Copper-Tolerant and Copper-Sensitive Strains of Pantoea ananatis

ABSTRACT A survey was conducted to evaluate differences in fatty acid methyl ester (FAME) profiles among strains of Pantoea ananatis, causal agent of center rot of onion (Allium cepa), isolated from 15 different onion cultivars in three different sites in Georgia. Differences in FAME composition were determined by plotting principal components (PCs) in two-dimensional plots. Euclidean distance squared (ED(2)) values indicated a high degree of similarity among strains. Plotting of PCs calculated from P. ananatis strains capable of growing on media amended with copper sulfate pentahydrate (200 mug/ml) indicated that copper-tolerant strains grouped into tight clusters separate from clusters formed by wild-type strains. However, unlike copper-sensitive strains, the copper-tolerant strains tended to cluster by location. A total of 80, 60, and 73% of the strains from Tift1, Tift2, and Tattnall, respectively, exhibited either confluent growth or partial growth on copper-amended medium. However, all strains were sensitive to a mixture of copper sulfate pentahydrate (200 mug/ml) and maneb (40 mug/ml). When copper-tolerant clones were analyzed and compared with their wild-type parents, in all cases the plotting of PCs developed from copper-tolerant clones formed tight clusters separate from clusters formed by the parents. Eigenvalues generated from these tests indicated that two components provided a good summary of the data, accounting for 98, 98, and 96% of the standardized variance for strains Pna 1-15B, Pna 1-12B, and Pna 2-5A, respectively. Furthermore, feature 4 (cis-9-hexadecenoic acid/2-hydroxy-13-methyltetradecanoic acid) and feature 7 (cis-9/trans-12/cis-7-octadecenoic acid) were the highest or second highest absolute values for PC1 in all three strains of the parents versus copper-tolerant clones, and hexadecanoic acid was the highest absolute value for PC2 in all three strains. Along with those fatty acids, dodecanoic acid and feature 3 (3-hydroxytetradecanoic acid/14-methylpentadecenoic acid) also had an impact on the differences observed between copper-sensitive parents and copper-resistant mutants. Finding these changes in bacterial fatty acid composition could lead to the development of a laboratory assay to identify copper-tolerant strains using gas chromatography as well as providing clues to further elucidate the mode of action of copper tolerance.

Species diversity and substrate utilization patterns of thermophilic bacterial communities in hot aerobic poultry and cattle manure composts

This study investigated the species diversity and substrate utilization patterns of culturable thermophilic bacterial communities in hot aerobic poultry and cattle manure composts by coupling 16S rDNA analysis with Biolog data. Based on the phylogenetic relationships of 16S rDNA sequences, 34 thermophilic (grown at 60 degrees C) bacteria isolated during aerobic composting of poultry manure and cattle manure were classified as Bacillus licheniformis, B. atrophaeus, Geobacillus stearothermophilus, G. thermodenitrificans, Brevibacillus thermoruber, Ureibacillus terrenus, U. thermosphaericus, and Paenibacillus cookii. In this study, B. atrophaeus, Br. thermoruber, and P. cookii were recorded for the first time in hot compost. Physiological profiles of these bacteria, obtained from the Biolog Gram-positive (GP) microplate system, were subjected to principal component analysis (PCA). All isolates were categorized into eight different PCA groups based on their substrate utilization patterns. The bacterial community from poultry manure compost comprised more divergent species (21 isolates, seven species) and utilized more diverse substrates (eight PCA groups) than that from cattle manure compost (13 isolates, five species, and four PCA groups). Many thermophilic bacteria isolated in this study could use a variety of carboxylic acids. Isolate B110 (from poultry manure compost), which is 97.6% similar to U. terrenus in its 16S rDNA sequence, possesses particularly high activity in utilizing a broad spectrum of substrates. This isolate may have potential applications in industry.

Chemical and biological characterization of slaughterhouse wastes compost

The chemical and biological properties of compost made from yard trimmings (YT) composted alone or mixed with slaughterhouse wastes (SHW) were evaluated in seven phases. Mixtures were weighed in a 2:1 proportion (YT:SHW) and placed in composting bins (0.91 m2). Temperature was recorded to determine the time (d) needed to reach the first (1HC) and second heat cycles (2HC). Composting characteristics were measured at 0 d, at the peak of the 1HC and 2HC, and at maturation (0, 20, 50 and 70 d). During 1HC, bacterial isolates were cultivated in both treatments and identified using the Biolog System. Chemical composition was statistically analyzed using a 2 (layers of SHW)x7 (composting phases) factorial arrangement of treatments with the ANOVA procedure of SAS. The pH was neutral for YT and ranged from 7.41 to 6.82 for SHW throughout the process. There was a decrease in organic matter (OM) and carbon (C), and a relative increase in nitrogen (N) in both treatments. At 70 d of maturation, C:N values were similar between treatments, but lower (P>0.05) than the initial values. Final N concentration was higher (P>0.05) for the treatment with SHW. Only the SHW treatment exhibited thermophilic temperatures. At the 1HC in both treatments, different populations of bacteria responsible for the breakdown of OM were identified showing an active heterogeneous population. The presence of pathogenic microorganisms was not detected in treatments containing SHW.

Microbial community growth and utilization of carbon constituents during thermophilic composting at different oxygen levels

Composting is characterized by dramatic changes in microbial community structure, to a high extent driven by changes in temperature and in the composition of the organic substrate. This study focuses on the interrelationships between decomposition of major classes in the organic material and dynamics in microbial populations during thermophilic composting of source-separated organic household waste. Experiments were performed in a 200-L laboratory reactor at 16, 2.5, and 1% O(2) in the compost atmosphere. Major classes of carbon constituents were analyzed by chemical methods, and the microbial biomass and community structure determined by fatty acid analyses with phospholipid fatty acids (PLFA) and total ester-linked fatty acids (EL) methods. At all three O(2) levels, the process was characterized by a rapid increase in microbial activity and biomass in the early thermophilic phase, although this period was delayed at the lower O(2) concentrations. Starch and fat were the main substrates utilized at all three O(2) levels during this period. The depletion of the starch fraction coincided with the beginning of a microbial biomass decrease, suggesting that starch is an important carbon substrate for the growth of thermophilic microorganisms during composting. Growth yields in the microbial community based on consumption of major carbon constituent classes in the high-activity period fell between 22 and 28%. Multivariate statistical analysis of changes in fatty acid composition revealed small, but statistically significant differences in the microbial community succession. At 16% O(2), 10 Me fatty acids from Actinomycetes and cyclopropyl fatty acids (from Gram-negative bacteria) became more important with time, whereas 18:1 omega 7t was characteristic at 2.5 and 1% O(2), indicating a more stressed bacterial community at the lower O(2) concentrations. Although adequate composting was achieved at O(2) levels as low as 2.5 and 1%, it is not recommended to compost at such low levels in large-scale systems, because the heterogeneous gas transport through the material in these systems might lead to anaerobic conditions and inefficient composting.

Microbial diversity in biodegradation and reutilization processes of garbage

With particular focus on the microbial diversity in garbage treatment, the current status of garbage treatment in Japan and microbial ecological studies on various bioprocesses for garbage treatment are described in detail. The future direction of research in this field is also discussed.

Microbial community dynamics during start-up operation of flowerpot-using fed-batch reactors for composting of household biowaste

Microbial community changes during start-up operation of flowerpot-using fed-batch reactors for composting of household biowaste were studied by quinone profiling, rRNA-targeted fluorescence in situ hybridization (FISH) and cultivation methods. Total and plate counts of bacteria and quinone contents in the reactors increased sharply with time during the start-up period. These increase patterns had two phases; the first increase occurred during 3-4 weeks from the start of waste loading and the second increase was found during the subsequent 4 weeks. The microbial biomass was temporally reduced between the two succession phases. Ubiquinones predominated at the beginning of operation but decreased sharply with time, whereas partially saturated menaquinones became predominant at the fully acclimated stage. These data indicated that the major constituents of microbial populations changed from ubiquinone-containing Proteobacteria to Actinobacteria during the period of operation. Neighbour-joining dendrograms constructed based on the quinone profile data suggested that at least one month is required to establish a stable community structure with the Actinobacteria predominating. The characteristic population shift in the start-up process was also demonstrated by FISH probing and 16S rDNA sequence comparisons of bacterial strains isolated.

Assessment of activated sludge microbial community analysis in full-scale biological wastewater treatment plants using patterns of fatty acid isopropyl esters (FAPEs)

This investigation introduces the application of a relatively rapid technique to obtain information about the dynamic nature of microbial communities in activated sludge. The objective has been to consider variability due to measurement errors and protocol changes within the same quantitative framework as the analysis of systematic differences in microbial communities in large-scale aerobic activated sludge secondary wastewater treatment systems. Adjustments to the methodology were considered due to their potential for simplifying and shortening the analysis procedure. All modifications to the protocols used to assay the composition of microbial fatty acids (MFAs) of activated sludge imposed some bias to the chromatographic data. This methodological bias was similar in magnitude to the level of discrimination between activated sludge microbial community structures that were considered as part of the present study. MFA analysis supported the expectations of subtle but systematic community structure differences and shifts in activated sludge based on the current understanding of these wastewater treatment systems. A standardized MFA methodology was shown to be sensitive to minor systematic changes in activated sludge communities due the anticipated underlying factors of selective pressures from the process configuration, history, operational conditions and/or nutrient status. The chemometric approach of fatty acid isopropyl ester analysis of activated sludge can provide a routine tool for meaningful and quantitative information of changes in activated sludge quality in full-scale treatment systems.

Microbiological aspects of biowaste during composting in a monitored compost bin

AIMS

To determine the microbial succession of the dominating taxa and functional groups of microorganisms and the total microbial activity during the composting of biowaste in a monitored process.

METHODS AND RESULTS

Biowaste (vegetable, fruit and garden waste) was composted in a monitored composting bin system. During the process, taxonomic and functional subpopulations of microorganisms were enumerated, and dominating colonies were isolated and identified. All counts decreased during the thermophilic phase of the composting, but increased again when the temperature declined. Total microbial activity, measured with an enzyme activity assay, decreased during the thermophilic phase, increased substantially thereafter, and decreased again during maturation. Bacteria dominated during the thermophilic phase while fungi, streptomycetes and yeasts were below the detection limit. Different bacterial populations were found in the thermophilic and mesophilic phases. In fresh wastes and during the peak-heating phase, all bacterial isolates were bacilli. During the cooling and maturation phase the bacterial diversity increased, including also other Gram-positive and Gram-negative bacteria. Among the fungi, Aspergillus spp. and Mucor spp. were predominant after the thermophilic phase.

CONCLUSIONS

The microbial abundance, composition and activity changed substantially during composting and compost maturity was correlated with high microbial diversity and low activity.

SIGNIFICANCE AND IMPACT OF THE STUDY

A more complete overview of the whole composting process of biowaste, based on microbial counts, species diversity and functional groups and abiotic parameters is presented, and the potential of a simple enzyme assay to measure total microbial activity was demonstrated.

Soil microbial community structure across a thermal gradient following a geothermal heating event

In this study microbial species diversity was assessed across a landscape in Yellowstone National Park, where an abrupt increase in soil temperature had occurred due to recent geothermal activity. Soil temperatures were measured, and samples were taken across a temperature gradient (35 to 65 degrees C at a 15-cm depth) that spanned geothermally disturbed and unimpacted soils; thermally perturbed soils were visually apparent by the occurrence of dead or dying lodgepole pine trees. Changes in soil microbial diversity across the temperature gradient were qualitatively assessed based on 16S rRNA sequence variation as detected by denaturing gradient gel electrophoresis (DGGE) using both ribosomal DNA (rDNA) and rRNA as PCR templates and primers specific for the Bacteria or Archaea domain. The impact of the major heating disturbance was apparent in that DGGE profiles from heated soils appeared less complex than those from the unaffected soils. Phylogenetic analysis of a bacterial 16S rDNA PCR clone library from a recently heated soil showed that a majority of the clones belonged to the Acidobacterium (51%) and Planctomyces (18%) divisions. Agar plate counts of soil suspensions cultured on dilute yeast extract and R2A agar media incubated at 25 or 50 degrees C revealed that thermophile populations were two to three orders of magnitude greater in the recently heated soil. A soil microcosm laboratory experiment simulated the geothermal heating event. As determined by both RNA- and DNA-based PCR coupled with DGGE, changes in community structure (marked change in the DGGE profile) of soils incubated at 50 degrees C occurred within 1 week and appeared to stabilize after 3 weeks. The results of our molecular and culture data suggest that thermophiles or thermotolerant species are randomly distributed in this area within Yellowstone National Park and that localized thermal activity selects for them.

Seasonal variation in microbial communities and organic malodor indicator compound concentrations in various types of swine manure storage systems

Anaerobic manure storage systems are one of the major contributors to the odor and environmental pollution associated with swine (Sus scrofa) production systems. The microbial ecology of manure storage systems and the relationships between microbial communities and odor production are largely unknown. In this study, we used community fatty acid methyl ester (FAME) analysis to generate lipid profiles to assess seasonal differences among microbial communities inhabiting various types of outdoor swine manure storage systems. Concurrently, we measured manure concentrations of several malodor indicator compounds as well as pH, temperature, and solids content. Principal components analysis (PCA) showed that there are differences in FAME profiles among the swine manure storage systems examined and most of the variation was in the relative abundance of 18:0, 18:1omega7t, 18:1omega7c/omega9t/omega12t, and 16:1omega7t/i15:0 2OH FAMEs. The PCA of the FAME profiles revealed that the phototrophic systems were more similar to each other and that the nonphototrophic systems were more similar to each other than they were to phototrophic lagoons. There were seasonal changes in the FAME profiles in the phototrophic systems and the concrete nonphototrophic basin (CNPB), and in one phototrophic system, the FAME profiles more closely resembled a CNPB FAME profile during the winter than the other phototrophic lagoons. In the phototrophic lagoon systems, there was a direct correlation between the abundance of the FAMEs identified in the PCA and manure concentrations of phenol, p-cresol, and 4-ethyl phenol. In the CNPB, there was a negative correlation between the total phenolics concentration and the 18:1omega7t FAME. Our results indicate that community FAME profiles could be used as a diagnostic tool for obtaining preliminary evidence that management practices are altering the system's microbial community to one that favors less air pollution potential.

Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA

High-temperature (>/=60 degrees C) synthetic food waste compost was examined by cultivation-dependent and -independent methods to determine predominant microbial populations. Fluorescent direct counts totaled 6.4 (+/-2.5)x10(10) cells gdw(-1) in a freeze-dried 74 degrees C compost sample, while plate counts for thermophilic heterotrophic aerobes averaged 2.6 (+/-1.0)x10(8) CFU gdw(-1). A pre-lysis cell fractionation method was developed to obtain community DNA and a suite of 16S and 18S rDNA-targeted PCR primers was used to examine the presence of Bacteria, Archaea and fungi. Bacterial 16S rDNA, including a domain-specific 1500-bp fragment and a 300-bp fragment specific for Actinobacteria, was amplified by PCR from all compost samples tested. Archaeal rDNA was not amplified in any sample. Fungal 18S rDNA was only amplified from a separate dairy manure compost that reached a peak temperature of 50 degrees C. Amplified rDNA restriction analysis (ARDRA) was used to screen isolated thermophilic bacteria and a clone library of full-length rDNA fragments. ARDRA screening revealed 14 unique patterns among 63 isolates, with one pattern accounting for 31 of the isolates. In the clone library, 52 unique patterns were detected among 70 clones, indicating high diversity of uncultivated bacteria in hot compost. Phylogenetic analysis revealed that the two most abundant isolates belonged in the genera Aneurinibacillus and Brevibacillus, which are not commonly associated with hot compost. With the exception of one Lactobacillus-type sequence, the clone library contained only sequences that clustered within the genus Bacillus. None of the isolates or cloned sequences could be assigned to the group of obligate thermophilic Bacillus spp. represented by B. stearothermophilus, commonly believed to dominate high-temperature compost. Amplified partial fragments from Actinobacteria, spanning the V3 variable region (Neefs et al. (1990) Nucleic Acids Res. 18, 2237-2242), included sequences related to the genera Saccharomonospora, Gordonia, Rhodococcus and Corynebacterium, although none of these organisms were detected among the isolates or full-length cloned rDNA sequences. All of the thermophilic isolates and sequenced rDNA fragments examined in this study were from Gram-positive organisms.

Microbial succession during a composting process as evaluated by denaturing gradient gel electrophoresis analysis

Microbial succession during a laboratory-scale composting process of garbage was analysed by denaturing gradient gel electrophoresis (DGGE) combined with measurement of physicochemical parameters such as temperature, pH, organic acids, total dissolved organic carbon and water-soluble humic substance. From the temperature changes, a rapid increase from 25 to 58 degrees C and then a gradual decrease, four phases were recognized in the process as follows; mesophilic (S), thermophilic (T), cooling (C) and maturing (M). The polymerase chain reaction-amplified 16S rDNA fragments with universal (907R) and eubacterial (341F with GC clamp) primers were subjected to DGGE analysis. Consequently, the DGGE band pattern changed during the composting process. The direct sequences from DGGE bands were related to those of known genera in the DNA database. The microbial succession determined by DGGE was summarized as follows: in the S phase some fermenting bacteria, such as lactobacillus, were present with the existing organic acids; in the T phase thermophilic bacillus appeared and, after the C phase, bacterial populations were more complex than in previous phases and the phylogenetic positions of those populations were relatively distant from strains so far in the DNA database. Thus, the DGGE method is useful to reveal microbial succession during a composting process.

Seasonal microbial community dynamics in a flowerpot-using personal composting system for disposal of household biowaste

Microbial community dynamics in a flowerpot-using solid biowaste composting (FUSBIC) process were monitored seasonally by quinone profiling and conventional microbiological methods. The FUSBIC system, which consisted of three flowerpots (14 L or 20 L capacity) with 5-6 kg each of a soil-compost mixture (SCM) as the primary reactors, was loaded daily with household biowaste from November 1998 to October 1999. The monthly average waste reduction rate was 88.2% for the 14-L system and 92.5% for the 20-L system on a wet weight basis. The direct total microbial count detected in the 14-L primary reactors ranged from 4.5 to 9.6x10(11) cells.g(-1) of dry wt of SCM, and the viable count of aerobic heterotrophic bacteria recovered on agar plates at 28 degrees C varied from 1.9 to 5.7x10(11) CFU.g(-1) of dry wt. The quinone content of SCM samples from the 14-L and 20-L systems ranged from 160 to 353 nmol.g(-1) of dry SCM. Ubiquinones, unsaturated menaquinones, and partially saturated menaquinones constituted 15.0-36.4, 14.8-22.0, and 41.8-61.6 mol% of the total content, respectively. The major quinone types detected were usually MK-8(H(2)), MK-9(H(2)), and Q-10. Variations in quinone profiles were evaluated numerically by using two parameters, the dissimilarity index (D) and microbial divergence index (MD(q)). The upper limit of seasonal changes in the microbial community structure was about 30% as expressed by D values. The MD(q) values calculated ranged from 18 to 22. A significant positive correlation was found between seasonal temperature and bacterial populations containing partially saturated menaquinones. These results indicated that the FUSBIC system contained highly diverse microbial populations that fluctuated to some extent depending on seasonal temperature. Members of the Actinobacteria were suggested to be the major constituents of the total population present.

Succession of microbial communities during hot composting as detected by PCR-single-strand-conformation polymorphism-based genetic profiles of small-subunit rRNA genes

A cultivation-independent technique for genetic profiling of PCR-amplified small-subunit rRNA genes (SSU rDNA) was chosen to characterize the diversity and succession of microbial communities during composting of an organic agricultural substrate. PCR amplifications were performed with DNA directly extracted from compost samples and with primers targeting either (i) the V4-V5 region of eubacterial 16S rRNA genes, (ii) the V3 region in the 16S rRNA genes of actinomycetes, or (iii) the V8-V9 region of fungal 18S rRNA genes. Homologous PCR products were converted to single-stranded DNA molecules by exonuclease digestion and were subsequently electrophoretically separated by their single-strand-conformation polymorphism (SSCP). Genetic profiles obtained by this technique showed a succession and increasing diversity of microbial populations with all primers. A total of 19 single products were isolated from the profiles by PCR reamplification and cloning. DNA sequencing of these molecular isolates showed similarities in the range of 92.3 to 100% to known gram-positive bacteria with a low or high G+C DNA content and to the SSU rDNA of gamma-Proteobacteria. The amplified 18S rRNA gene sequences were related to the respective gene regions of Candida krusei and Candida tropicalis. Specific molecular isolates could be attributed to different composting stages. The diversity of cultivated bacteria isolated from samples taken at the end of the composting process was low. A total of 290 isolates were related to only 6 different species. Two or three of these species were also detectable in the SSCP community profiles. Our study indicates that community SSCP profiles can be highly useful for the monitoring of bacterial diversity and community successions in a biotechnologically relevant process.

Increase in bacterial community diversity in subsurface aquifers receiving livestock wastewater input

Despite intensive studies of microbial-community diversity, the questions of which kinds of microbial populations are associated with changes in community diversity have not yet been fully solved by molecular approaches. In this study, to investigate the impact of livestock wastewater on changes in the bacterial communities in groundwater, bacterial communities in subsurface aquifers were analyzed by characterizing their 16S rDNA sequences. The similarity coefficients of restriction fragment length polymorphism (RFLP) patterns of the cloned 16S ribosomal DNAs showed that the bacterial communities in livestock wastewater samples were more closely related to those in contaminated aquifer samples. In addition, calculations of community diversity clearly showed that bacterial communities in the livestock wastewater and the contaminated aquifer were much more diverse than those in the uncontaminated aquifer. Thus, the increase in bacterial-community diversity in the contaminated aquifer was assumed to be due to the infiltration of livestock wastewater, containing high concentrations of diverse microbial flora, into the aquifer. Phylogenetic analysis of the sequences from a subset of the RFLP patterns showed that the Cytophaga-Flexibacter-Bacteroides and low-G+C gram-positive groups originating from livestock wastewater were responsible for the change in the bacterial community in groundwater. This was evidenced by the occurrence of rumen-related sequences not only in the livestock wastewater samples but also in the contaminated-groundwater samples. Rumen-related sequences, therefore, can be used as indicator sequences for fecal contamination of groundwater, particularly from livestock.