Nematode inhibiting organic materials and a strain of Trichoderma harzianum effectively manages Meloidogyne incognita in Withania somnifera fields

The usefulness of Trichoderma harzianum was tested along with farmyard manure, cow urine, neem oil seed cake, and vermicompost separately and in combination to manage Meloidogyne incognita in Withania somnifera. A treatment combination of nematode inhibitory vermicompost and T. harzianum was found to be most effective against M. incognita.     

Influence of organic and inorganic sources of nutrients on the functional diversity of microbial communities in the vegetable cropping system of the Indo-Gangetic plains

The aim of the present study was to assess the effects of different organic and inorganic fertilizers on the functional diversity of soil microbial community under a vegetable production system. The Biolog^® Eco-plate technique and indices, such as average well-colour development (AWCD), McIntosh and Shannon diversity were employed to study the diversity of soil microorganisms. The AWCD, i.e. overall utilization of carbon sources, suggested that different organic treatments had a significant impact on the metabolic activity of soil microorganisms. After 120 h, the highest AWCD values were observed in poultry manure (2.5 t·ha^?1) + vermicompost (3.5 t·ha^?1) (0.63) and farm yard manure (FYM) (10 t·ha^?1) + vermicompost (3.5 t·ha^?1) (0.61). After 72 h, the highest value of the McIntosh diversity index was recorded in poultry manure (2.5 t·ha^?1) + vermicompost (3.5 t·ha^?1) (3.87), followed by poultry manure (2.5 t·ha^?1) + vermicompost (3.5 t·ha^?1) + biofertilizers (Azotobacter 500 g·ha^?1 applied as seed treatment) (3.12). In the case of the Shannon diversity index, the highest values were noticed in organic treatments; however, there was no significant differences between organic and inorganic treatments. Biplot analysis showed a clear differentiation of organic treatments from the inorganic control. The amino acids, phenolics and polymer utilizing microorganisms were dominant in organic treatments. Inorganic control recorded the lowest values of the microbial diversity indices. Through this study, we have identified the best combination of organic nutrients, i.e. poultry manure (2.5 t·ha^?1) + vermicompost (3.5 t·ha^?1) for the stimulation of metabolically active soil microbial communities.     

Potential of Allolobophora parva (Oligochaeta) in vermicomposting

The aim of this study was to assess the potential of Allolobophora parva Eisen as a candidate for vermicomposting practices. Five organic waste mixtures: cow dung (CD), biogas plant slurry (BGS), cow dung + vegetable waste (CD + VW), BGS + VW and VW + Soil were vermicomposted using A. parva. Vermicomposting showed a decrease in pH, organic C and C:N ratio, but increase total N, available P and exchangeable K at the end. C:N ratio of end material (vermicompost) was within the agronomic acceptable limit (<20). The high level of NPK in worm-processed material indicates the candidature of this species for waste management operations. The earthworm also showed an excellent growth in different wastes. Results thus indicate that A. parva appeared a potential tool for conversion of organic wastes into value added products for sustainable land restoration practices.     

Aerobic heterotrophic bacteria and petroleum-utilizing bacteria from cow dung and poultry manure

In this study, enumeration and identification of total aerobic heterotrophic bacteria and petroleum-utilizing bacteria as well as the degradative potential of petroleum-utilizing bacterial isolates were carried out. The average counts of total aerobic heterotrophic bacteria in cow dung and poultry manure were 74.25 × 10⁵ c.f.u. g⁻¹ and 138.75 × 10⁵ c.f.u. g⁻¹ respectively. Acinetobacter sp, Bacillus sp, Pseudomonas sp, and Serratia spp. occurred as aerobic heterotrophs in both cow dung and poultry manure. However, Alcaligenes spp. occurred only in cow dung while, Flavobacterium sp, Klebsiella sp, Micrococcus sp, and Nocardia spp. occurred only in poultry manure as aerobic heterotrophs. The average counts of petroleum-utilizing bacteria in cow dung and poultry manure were 9.25 × 10⁵ c.f.u. g⁻¹ and 17.25 × 10⁵ c.f.u. g⁻¹ respectively. Pseudomonas spp. occurred as petroleum utilizer in both cow dung and poultry manure. However, Bacillus spp. occurred only in cow dung while Acinetobacter spp. and Micrococcus spp. occurred only in poultry manure as petroleum utilizers. Relative abundance of petroleum utilizers in total aerobic heterotrophs ranged from 6.38% to 20.00% for cow dung and from 9.38% to 17.29% for poultry manure. Introduction of pure cultures of petroleum-utilizing bacteria from cow dung and poultry manure into sterile oil-polluted soil revealed oil degradation in one week period.     

有机物料种类及腐熟水平对土壤微生物群落的影响

应用Biolog方法研究了温室盆栽番茄条件下,施用不同种类及不同腐熟水平的有机物料对土壤微生物群落的影响,施用有机物料60d后取土分析土壤微生物群落多样性及土壤微生物对Biolog微平板中胺、氨基酸、糖、羧酸、聚合物和其它类碳源的利用情况,结果表明,施用有机物料可提高土壤微生物群落多样性,施用新鲜酒糟的多样性指数略高于施用腐熟10d酒糟,牛粪不同腐熟水平对多样性影响显著,且对多样性具有正向或负向的影响;对照和施用酒糟的土壤微生物对聚合物的利用率高于施用牛粪处理,施用新鲜物料处理的土壤微生物对聚合物的利用率高于施用腐熟物料处理。     

Molecular-based environmental risk assessment of three varieties of genetically engineered cows

The development of animal biotechnology has led to an increase in attention to biosafety issues. Here we evaluated the impact of genetically engineered cows on the environment. The probability of horizontal gene transfer and the impact on the microbial communities in cow gut and soil were tested using three varieties of genetically engineered cows that were previously transformed with a human gene encoding lysozyme, lactoferrin, or human alpha lactalbumin. The results showed that the transgenes were not detectable by polymerase chain reaction (PCR) or quantitative real-time PCR in gut microbial DNA extracts of manure or microbial DNA extracts of topsoil. In addition, the transgenes had no impact on the microbial communities in cow gut or soil as assessed by PCR-denaturing gradient gel electrophoresis or 16S rDNA sequencing. Furthermore, phylogenetic analyses showed that the manure bacteria sampled during each of the four seasons belonged primarily to two groups, Firmicutes and Bacteroidetes, and the soil bacteria belonged to four groups, Firmicutes, Bacteroidetes, Actinobacteria, and α-proteobacteria. Other groups, such as β-proteobacteria, γ-proteobacteria, δ-proteobacteria, ε-proteobacteria, Spirochaetes, Acidobacteria, Chloroflexi, and Nitrospira, were not dominant in the manure or soil.     

Changes in Bacterial and Fungal Communities across Compost Recipes,Preparation Methods,and Composting Times

Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties.     

Storage conditions and animal source influence the dominant bacterial community composition in animal manure

The aim of this study was to determine the impact of storage, animal diet, and animal source on the bacterial community composition of manure. The differences among bacterial community structures in fresh manure from cows on two different diets, cow manure stored in a deep pit for about one month, and fresh pig manure were compared. A molecular approach consisting of terminal restriction fragment length polymorphism (T-RFLP), in combination with sequence information from clone libraries, facilitated the identification of specific dominant bacterial populations that varied significantly among manures from different sources and treatments. One such population, represented by TRF 157, the most dominant peak of the bacterial community from stored manure, was identified as a Spirochaeta sp. Interestingly, this peak was absent in the fresh manure communities. The prevailing species in the fresh manure bacterial communities were distinct from those in manure from the storage pit, indicating a major shift in bacterial community composition induced by storage conditions. Moreover, distinct differences in bacterial communities were observed among animal source, but not animal feed. Manure storage is consequently an important parameter to consider when handling fertilizers, in order to obtain an optimal soil microbial ecosystem functioning.     

Temporal dynamics of microbial communities in microcosms in response to pollutants

Elucidating the mechanisms underlying microbial succession is a major goal of microbial ecology research. Given the increasing human pressure on the environment and natural resources, responses to the repeated introduction of organic and inorganic pollutants are of particular interest. To investigate the temporal dynamics of microbial communities in response to pollutants, we analysed the microbial community structure in batch microcosms that were inoculated with soil bacteria following exposure to individual or combined pollutants (phenanthrene, n‐octadecane, phenanthrene + n‐octadecane and phenanthrene + n‐octadecane + CdCl₂). Subculturing was performed at 10‐day intervals, followed by high‐throughput sequencing of 16S rRNA genes. The dynamics of microbial communities in response to different pollutants alone and in combination displayed similar patterns during enrichment. Specifically, the repression and induction of microbial taxa were dominant, and the fluctuation was not significant. The rate of appearance for new taxa and the temporal turnover within microbial communities were higher than the rates reported in other studies of microbial communities in air, water and soil samples. In addition, conditionally rare taxa that were specific to the treatments exhibited higher betweenness centrality values in the co‐occurrence network, indicating a strong influence on other interactions in the community. These results suggest that the repeated introduction of pollutants could accelerate microbial succession in microcosms, resulting in the rapid re‐equilibration of microbial communities.     

Microbial community structure in anaerobic co-digestion of grass silage and cow manure in a laboratory continuously stirred tank reactor

The impacts of feeding ratio and loading rate on the microbial community during co-digestion of grass silage with cow manure in an anaerobic laboratory continuously stirred tank reactor were investigated by 16S rRNA gene-based fingerprints. The microbial community remained stable when the reactor was fed with cow manure alone and with up to 20% of grass silage in feedstock at an organic loading rate (OLR) of 2 kg VS m⁻³ day⁻¹. Large changes in the bacterial community were observed when the loading ratio of grass was increased to 40%, while there was little change in the archaeal community. During the increase in OLR from 2 to 4 kg VS m⁻³ day⁻¹ the bacterial community structure showed few differences, whereas Archaea was undetectable. Sequencing of the major DGGE bands indicated that the phylum Bacteriodetes predominated in the bacterial community. Two unclassified bacteria with high abundance survived throughout the operation of the reactor.     

Pig manure vermicompost as a component of a horticultural bedding plant medium: effects on physicochemical properties and plant growth

This experiment was designed to characterize the physical, chemical and microbial properties of a standard commercial horticultural, greenhouse container, bedding plant medium (Metro-Mix 360), that had been substituted with a range of increasing concentrations (0%, 5%, 10%, 25%, 50% and 100% by volume) of pig manure vermicompost and to relate these properties to plant growth responses. The growth trials used tomatoes (Lycopersicon esculentum Mill.), grown in the substituted media for 31 days under glasshouse conditions, with seedling growth recorded in 20 pots for each treatment. Half of the tomato seedlings (10 pots per treatment) were watered daily with liquid inorganic fertilizer while the other half received water only. The percentage total porosity, percentage air space, pH and ammonium concentrations of the container medium all decreased significantly, after substitution of Metro-Mix 360 with equivalent amounts of pig manure vermicompost; whereas bulk density, container capacity, electrical conductivity, overall microbial activity and nitrate concentrations, all increased with increasing substitutions of vermicompost. The growth of tomato seedlings in the potting mixtures containing 100% pig manure vermicompost was reduced, possibly as a result of high soluble salt concentrations in the vermicompost and poorer porosity and aeration. The growth of tomato seedlings was greatest after substitution of Metro-Mix 360 with between 25% and 50% pig manure vermicompost, with more growth occurring in combinations of pig manure vermicompost treated regularly with a liquid fertilizer solution than in those with no fertilizer applied. Some of the growth enhancement in these mixtures seemed to be related to the combined effects of improved porosity, aeration and water retention in the medium and the high nitrate content of the substrate, which produced an increased uptake of nitrogen by the plant tissues, resulting in increased plant growth. When the tomato seedlings were watered daily with liquid inorganic fertilizer, substitution of Metro-Mix 360 with a very small amount (5%) of pig manure vermicompost resulted in a significant increase in the growth of tomato seedlings. Such effects could not be attributed solely to the nutritional or physical properties of the pig manure vermicompost. Therefore, it seems likely that the pig manure vermicompost provided other biological inputs, such as plant growth regulators into the container medium, that still need to be identified fully.     

Evaluating the prevalence and genetic diversity of adenovirus and polyomavirus in bovine waste for microbial source tracking

This study evaluated and compared the occurrence, concentrations, and genetic diversity of bovine polyomavirus (BPyV) and bovine adenovirus (BAdV) in manure and feces samples for the purpose of determining which of these two viruses is more suitable for bovine fecal indication and microbial source tracking. The comparability and correlation between concentrations/prevalence of these viruses and bacterial fecal indicators (cow-associated Bacteroidetes, Escherichia coli and enterococci) in manure and fecal samples was also determined. A total of 26 dairy manure and 18 individual dairy cow feces samples were tested. The results showed the mean concentration of BAdV in all of dairy manure samples was at least 1 log lower than BPyV (p ≤ 0.005). All of the dairy manure samples tested positive for BPyV but not for BAdV. After combining dairy manure measurements, bacterial indicators had 0.3–0.7 log (p ≤ 0.05) and 1.8–2.2 log (p ≤ 0.005) higher concentrations than BPyV and BAdV, respectively. The concentration of BPyV had a significant positive correlation with the concentration of E. coli and enterococci in the manure samples. The partial VP1 genetic sequences of BPyV isolated from three different farms had a 100% homology to each other and to VP1 sequence (D13942.1) reported in previous study. Based on the occurrence, quantitative and genetic diversity results, BPyV may be a better indicator than BAdV for microbial source tracking at manure application sites.     

Bacterial diversity in a finished compost and vermicompost: differences revealed by cultivation-independent analyses of PCR-amplified 16S rRNA genes

Bacterial communities are important catalysts in the production of composts. Here, it was analysed whether the diversity of bacteria in finished composts is stable and specific for the production process. Single-strand conformation polymorphism (SSCP) based on polymerase chain reaction amplified partial 16S rRNA genes was used to profile and analyse bacterial communities found in total DNA extracted from finished composts. Different batches of compost samples stored over a period of 12 years and a 1-year-old vermicompost were compared to each other. According to digital image analysis, clear differences could be detected between the profiles from compost and vermicompost. Differences between three different periods of compost storage and between replicate vermicompost windrows were only minor. A total of 41 different 16S rRNA genes were identified from the SSCP profiles by DNA sequencing, with the vast majority related to yet-uncultivated bacteria. Sequences retrieved from compost mainly belonged to the phyla Actinobacteria and Firmicutes. In contrast, vermicompost was dominated by bacteria related to uncultured Chloroflexi, Acidobacteria, Bacteroidetes and Gemmatimonadetes. The differences were underscored with specific gene probes and Southern blot hybridizations. The results confirmed that different substrates and composting processes selected for specific bacterial communities in the finished products. The specificity and consistency of the bacterial communities inhabiting the compost materials suggest that cultivation-independent bacterial community analysis is a potentially useful indicator to characterize the quality of finished composts in regard to production processes and effects of storage conditions.     

Organic Amendments Improve Plant Morpho-Physiology and Antioxidant Metabolism in Mitigating Drought Stress in Bread Wheat (<i>Triticum aestivum</i> L.)

Due to the unpredictable climate change, drought stress is being considered as one of the major threats to crop production. Wheat (Triticum aestivum L. cv. BARI Gom-26) being a dry season crop frequently faces scarcity of water and results in a lower yield. Therefore, this experiment aims to explore the role of different organic amendments (OAs) in mitigating drought stress-induced damage. The pot experiment consisted of different organic amendments viz. compost, vermicompost and poultry manure @0.09 kg m⁻² soil, biochar @2.5% w/w soil and chitosan @1% w/w soil which was imposed on the plants grown under both well-watered and drought conditions. Results showed that drought stress reduced plant height (15%), SPAD value (16%), relative water content (13%), number of spikelet spike⁻¹ (17%), number of grains spike⁻¹ (12%), and 100-grain weight (18%). Organic amendments act as a protectant and reduce drought stress-induced damages by enhancing the morpho-physiological and yield attributes. Vermicompost enhanced SPAD value by 18%, number of spikelets spike⁻¹ by 20%, number of grains spike⁻¹ by 17%, whereas poultry manure increased plant height by 16% under drought condition compared to control plant. Unlike other OAs applied, vermicompost was proved to be capable of reducing the higher lipid peroxidation and proline content raised by drought condition. Drought stress-induced increment of catalase, ascorbate peroxidase and glutathione reductase activities were also efficiently modulated by the organic amendment application. The present study concluded that OAs play significant roles in alleviating drought stressinduced damages by improving the morpho-physiological attributes and among the different types of OAs used vermicompost performed better which in addition ceased the production of reactive oxygen species.     

Air-side ammonia stripping coupled to anaerobic digestion indirectly impacts anaerobic microbiome

Air-side stripping without a prior solid–liquid phase separation step is a feasible and promising process to control ammonia concentration in thermophilic digesters. During the process, part of the anaerobic biomass is exposed to high temperature, high pH and aerobic conditions. However, there are no studies assessing the effects of those harsh conditions on the microbial communities of thermophilic digesters. To fill this knowledge gap, the microbiomes of two thermophilic digesters (55°C), fed with a mixture of pig manure and nitrogen-rich co-substrates, were investigated under different organic loading rates (OLR: 1.1–5.2 g COD l⁻¹ day⁻¹), ammonia concentrations (0.2–1.5 g free ammonia nitrogen l⁻¹) and stripping frequencies (3–5 times per week). The bacterial communities were dominated by Firmicutes and Bacteroidetes phyla, while the predominant methanogens were Methanosarcina sp archaea. Increasing co-substrate fraction, OLR and free ammonia nitrogen (FAN) favoured the presence of genera Ruminiclostridium, Clostridium and Tepidimicrobium and of hydrogenotrophic methanogens, mainly Methanoculleus archaea. The data indicated that the use of air-side stripping did not adversely affect thermophilic microbial communities, but indirectly modulated them by controlling FAN concentrations in the digester. These results demonstrate the viability at microbial community level of air side-stream stripping process as an adequate technology for the ammonia control during anaerobic co-digestion of nitrogen-rich substrates.     

Chemical and microbiological changes during vermicomposting of coffee pulp using exotic (<Emphasis Type="Italic">Eudrilus eugeniae</Emphasis>) and native earthworm (<Emphasis Type="Italic">Perionyx ceylanesis</Emphasis>) species

Coffee pulp is the main solid residue from the wet processing of coffee berries. Due to presence of anti-physiological and anti-nutritional factors, coffee pulp is not considered as adequate substrate for bioconversion process by coffee farmers. Recent stringent measures by Pollution Control authorities, made it mandatory to treat all the solid and liquid waste emanating from the coffee farms. A study was conducted to evaluate the efficiency of an exotic (Eudrilus eugeniae) and a native earthworm (Perionyx ceylanesis) from coffee farm for decomposition of coffee pulp into valuable vermicompost. Exotic earthworms were found to degrade the coffee pulp faster (112 days) as compared to the native worms (165 days) and the vermicomposting efficiency (77.9%) and vermicompost yield (389 kg) were found to significantly higher with native worms. The multiplication rate of earthworms (280%) and worm yield (3.78 kg) recorded significantly higher with the exotic earthworms. The percentage of nitrogen, phosphorous, potassium, calcium and magnesium in vermicompost was found to increase while C:N ratio, pH and total organic carbon declined as a function of the vermicomposting. The plant nutrients, nitrogen (80.6%), phosphorus (292%) and potassium (550%) content found to increase significantly in the vermicompost produced using native earthworms as compared to the initial values, while the calcium (85.7%) and magnesium (210%) content found to increase significantly in compost produced utilizing exotic worms. Vermicompost and vermicasts from native earthworms recorded significantly higher functional microbial group’s population as compared to the exotic worms. The study reveals that coffee pulp can be very well used as substrate for vermicomposting using exotic (Eudrilus eugeniae) and native earthworm (Perionyx ceylanesis).     

Assessing the impact of composting and vermicomposting on bacterial community size and structure, and microbial functional diversity of an olive-mill waste

The aim of this study was to couple biochemical and molecular methodologies for evaluating the impact of two recycling technologies (composting and vermicomposting) on a toxic organic waste. To do this, six enzyme activities controlling the key metabolic pathways of the breakdown of organic matter, real-time PCR assays targeting 16S rRNA genes, and denaturing gradient gel electrophoresis (DGGE) profiling-sequence analysis of PCR-amplified 16S rRNA fragments have been used to determine the functional diversity, bacterial number, and bacterial community structure, respectively, in a mixture of olive waste and sheep manure, and in the derived compost and vermicompost. Both the recycling technologies were effective in activating the microbial parameters of the toxic waste, the vermicomposting being the best process to produce greater bacterial diversity, greater bacterial numbers and greater functional diversity. Although several identical populations were detected in the processed and non-processed materials, each technology modified the original microbial communities of the waste in a diverse way, indicating the different roles of each one in the bacterial selection.     

Enhancing the biomethane potential of liquid dairy cow manure by addition of solid manure fractions

Objectives

To assess the effect of adding solid manure fractions on the biomethane potential (BMP) of liquid dairy cow manure and on the biokinetic parameters of the process.

Results

The methanogenic potential of liquid dairy cow manure was strongly effected by adding a solid manure fraction. The 90/10 % (w/w) liquid/solid manure fraction mixture was the best substrate for CH₄ production. This substrate mixture improved by 50 % the final CH₄ production per g substrate and decreased the lag time by 220 % relative to the reference BMP test without the addition. Moreover, the addition of 20 % solid manure fraction adversely affected both the final CH₄ production and the maximum methane production rate, while increased the lag time by 400 % compared to the reference BMP test without addition.

Conclusions

Liquid dairy cow manure should be supplemented with no more than 10 % of solid manure fraction in order to improve the biomethane potential of this important agro-industrial residue.

     

Effectiveness of biochar and compost on improving soil hydro-physical properties,crop yield and monetary returns in inceptisol subtropics

Organic manures in combination with biochar might improve efficacy of biochar in improving soil functions related to hydro-physical properties and a field experiment was conducted over the course of two years with two levels of biochar @ 0 and 2tha⁻¹ and four levels of compost (100% recommended dose of N through farm yard manure, 100% recommended dose of N through vermicompost, 50% recommended dose of N through farm yard manure, and vermicompost each, and unfertilized control). Each treatment was replicated three times in factorial randomized block design (RBD). The objective of this research was to determine the effects of biochar and compost on soil hydro-physical properties, water use efficiency, monetary returns and yield of knolkhol (Brassica oleracea var. gongyloides L.) under sub-tropics of North West India. Compared with no-biochar, application of biochar significantly increased knolkhol yield by 7.8% and soil properties (infiltration rate, aggregate stability, maximum water holding capacity and hydraulic conductivity). Similarly, integration of compost significantly enhanced the soil water retention, aggregate stability, hydraulic conductivity and crop yield and gave highest infiltration rate, water retention, hydraulic conductivity and crop yield under M3 (50 % N through farm yard manure, +50 % N through vermicompost) treatment. Furthermore, synergetic positive effect of biochar and compost were noted for soil infiltration rate (4–38%), water retention (0.9–13.7%), aggregate stability (6–10.7%) and yield (6–11.9%) over the sole application of compost. Combined use of farm yard manure, and vermicompost accompanied by biochar resulted in highest net returns and B:C ratio. Biochar in combination with farm yard manure, and vermicompost can enhance soil hydraulic properties resulting in increased crop yield and maximum monetary returns under subtropical conditions.