Two-phase olive mill waste composting: community dynamics and functional role of the resident microbiota

Microbiomes of urban trees: unveiling contributions to atmospheric pollution mitigation

Urban trees are crucial in delivering essential ecosystem services, including air pollution mitigation. This service is influenced by plant associated microbiomes, which can degrade hydrocarbons, support tree health, and influence ecological processes. Yet, our understanding of tree microbiomes remains limited, thus affecting our ability to assess and quantify the ecosystem services provided by trees as complex systems. The main hypothesis of this work was that tree microbiomes concur to hydrocarbon biodegradation, and was tested through three case studies, which collectively investigated two tree micro-habitats (phyllosphere and tree cavity organic soil-TCOS) under various conditions representing diverse ecological scenarios, by applying different culture-based and molecular techniques and at different scales. The integration of all results provided a more comprehensive understanding of the role of microbiomes in urban trees. Firstly, bacterial strains isolated from the phyllosphere of Quercus ilex were characterized, indicating the presence of Plant-Growth Promoting bacteria and strains able to catabolize PAHs, particularly naphthalene and phenanthrene. Secondly, naphthalene biodegradation on artificially spiked Hedera helix leaves was quantified in greenhouse experiments on inoculated and untreated plants. The persistence of the inoculated strain and community structure of epiphytic bacteria were assessed by Illumina sequencing of V5-V6 hypervariable regions of 16S rRNA gene. Results showed that naphthalene degradation was initially faster on inoculated plants but later the degradation rates became similar, probably because bacterial populations with hydrocarbon-degrading abilities gradually developed also on non-inoculated plants. Finally, we explored bacterial and fungal biodiversity hosted by TCOS samples, collected from six large trees located in an urban park and belonging to different species. Microbial communities were characterized by Illumina sequencing of V5-V6 hypervariable regions of bacterial gene 16S rRNA and of fungal ITS1. Results indicated TCOS as a distinct substrate, whose microbiome is determined both by the host tree and by canopy environmental conditions and has a pronounced aerobic hydrocarbon degradation potential. Overall, a better assessment of biodiversity associated with trees and the subsequent provision of ecosystem services constitute a first step toward developing future new microbe-driven sustainable solutions, especially in terms of support for urban green planning and management policy.

Converting kitchen waste into value-added fertilizer using thermophilic semi-continuous composting-biofiltration two-stage process with minimized NH3 emission

Thermophilic semi-continuous composting (TSC) is effective for kitchen waste (KW) treatment, but large amounts of NH3-rich odorous gas are generated. This study proposes a TSC-biofiltration (BF) two-stage process. Compost from the front-end TSC was used as the packing material in the BF to remove NH3 from the exhaust gas. The BF process was effective in removing up to 83.7 % of NH3, and the NH3 content was reduced to < 8 ppm. Seven days of BF improved the quality of the product from TSC by enhancing the germination index to 134.6 %, 36.5 % higher than that in the aerated-only group. Microbial community analysis revealed rapid proliferation and eventual dominance in the BF of members related to compost maturation and the nitrogen cycle from Actinobacteria, Proteobacteria, Chloroflexi, and Bacteroidetes. The results suggest that the TSC-BF two-stage process is effective in reducing NH3 emissions from TSC and improving compost quality.

Composition, structure, and functional shifts of prokaryotic communities in response to co-composting of various nitrogenous green feedstocks

BACKGROUND

Thermophilic composting is a promising method of sanitizing pathogens in manure and a source of agriculturally important thermostable enzymes and microorganisms from organic wastes. Despite the extensive studies on compost prokaryotes, shifts in microbial profiles under the influence of various green materials and composting days are still not well understood, considering the complexity of the green material sources. Here, the effect of regimens of green composting material on the diversity, abundance, and metabolic capacity of prokaryotic communities in a thermophilic compost environment was examined.

METHODS

Total community 16S rRNA was recovered from triplicate compost samples of Lantana-based, Tithonia-based, Grass-based, and mixed (Lantana + Tithonia + Grass)- based at 21, 42, 63, and 84 days of composting. The 16S rRNA was sequenced using the Illumina Miseq platform. Bioinformatics analysis was done using Divisive Amplicon Denoising Algorithm version 2 (DADA2) R version 4.1 and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States version 2 (PICRUSt2) pipelines for community structure and metabolic profiles, respectively. In DADA2, prokaryotic classification was done using the Refseq-ribosomal database project (RDP) and SILVA version 138 databases.

RESULTS

Our results showed apparent differences in prokaryotic community structure for total diversity and abundance within the four compost regimens and composting days. The study showed that the most prevalent phyla during composting included Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexi, and Proteobacteria. Additionally, there were differences in the overall diversity of metabolic pathways but no significant differences among the various compost treatments on major metabolic pathways like carbohydrate biosynthesis, carbohydrate degradation, and nitrogen biosynthesis.

CONCLUSION

Various sources of green material affect the succession of compost nutrients and prokaryotic communities. The similarity of amounts of nutrients, such as total Nitrogen, at the end of the composting process, despite differences in feedstock material, indicates a significant influence of composting days on the stability of nutrients during composting.

Treatment technologies for olive mill wastewater with impacts on plants

Olive mill wastewater (OMW), produced during olive oil production, contains high levels of salt contents, organic matter, suspended particles, and toxic chemicals (particularly phenols), which all result in increased biological and chemical oxygen demand. Olive Oil Mills' Wastes (OMW), which have dark brown color with unpleasant smell, consist mainly of water, high organic (mainly phenols and polyphenols) and low inorganic compounds (e.g. potassium and phosphorus), as well as grease. OMW components can negatively affect soil's physical, chemical, and biological properties, rendering it phytotoxic. However, OMW can positively affect plants' development when it's applied to the soil after pretreatment and treatment processes due to its high mineral contents and organic matter. There are various approaches for removing impurities and the treatment of OMW including chemical, biological, thermal, physiochemical, and biophysical processes. Physical techniques involve filtration, dilution, and centrifugation. Thermal methods include combustion and pyrolysis; biological techniques use anaerobic and aerobic techniques, whereas adsorption and electrocoagulation act as physiochemical methods, and coagulation and flocculation as biophysical methods. In contrast, combined biological treatment methods use co-digestion and composting. A comparison of the effects of both treated and untreated OMW samples on plant development and soil parameters can help us to understand the potential role of OMW in increasing soil fertility. This review discusses the impacts of untreated OMW and treated OMW in terms of soil characteristics, seed germination, and plant growth. This review summarizes all alternative approaches and technologies for pretreatment, treatment, and recovery of valuable byproducts and reuse of OMW across the world.

Preparation, biocontrol activity and growth promotion of biofertilizer containing Streptomyces aureoverticillatus HN6

Nowadays, due to the excessive dependence on chemical fertilizers and pesticides in agricultural production, many problems, such as soil hardening and soil-borne diseases, have become increasingly prominent, which seriously restrict the sustainable development of agriculture. The application of microbial fertilizer prepared by biocontrol microorganisms can not only improve soil structure and increase fertility but also have the function of controlling diseases. Streptomyces aureoverticillatus HN6 has obvious disease prevention and growth promotive effect, which can improve the rhizosphere fertility of plants and even regulate the rhizosphere microbial community of plants. Based on the comparison of frame composting and natural composting, we used the response surface method to optimize the preparation conditions of Streptomyces HN6 bacterial fertilizer. The results showed that natural composting not only produced higher composting temperatures and maintained long high temperature periods in accordance with local conditions, but was also more suitable for composting in the field according to local conditions. Therefore, the substrate's conductivity changed more, the ash accumulation increased, and the substrate decomposed more thoroughly. Thus, this composting method is highly recommended. Additionally, Streptomyces HN6 microbial fertilizer EC20 can reduce cowpea fusarium wilt and promote cowpea growth. The number of plant leaves, plant height and fresh weight, increased significantly in the microbial fertilizer EC20. Moreover, Streptomyces HN6 fertilizer EC20 could significantly induce soil invertase, urease and catalase activities. Our study highlights the potential use of Streptomyces HN6 as a biofertilizer to improve plant productivity and biological control of plant pathogenic fungi.

Recent advances in metagenomic analysis of different ecological niches for enhanced biodegradation of recalcitrant lignocellulosic biomass

Lignocellulose wastes stemming from agricultural residues can offer an excellent opportunity as alternative energy solutions in addition to fossil fuels. Besides, the unrestrained burning of agricultural residues can lead to the destruction of the soil microflora and associated soil sterilization. However, the difficulties associated with the biodegradation of lignocellulose biomasses remain as a formidable challenge for their sustainable management. In this respect, metagenomics can be used as an effective option to resolve such dilemma because of its potential as the next generation sequencing technology and bioinformatics tools to harness novel microbial consortia from diverse environments (e.g., soil, alpine forests, and hypersaline/acidic/hot sulfur springs). In light of the challenges associated with the bulk-scale biodegradation of lignocellulose-rich agricultural residues, this review is organized to help delineate the fundamental aspects of metagenomics towards the assessment of the microbial consortia and novel molecules (such as biocatalysts) which are otherwise unidentifiable by conventional laboratory culturing techniques. The discussion is extended further to highlight the recent advancements (e.g., from 2011 to 2022) in metagenomic approaches for the isolation and purification of lignocellulolytic microbes from different ecosystems along with the technical challenges and prospects associated with their wide implementation and scale-up. This review should thus be one of the first comprehensive reports on the metagenomics-based analysis of different environmental samples for the isolation and purification of lignocellulose degrading enzymes.

Biorecovery of olive mill wastewater sludge from evaporation ponds

Olive mill wastewater (OMW) resulting from the olive oil extraction process is usually disposed of in evaporation ponds where it concentrates generating a sludge that pollutes the ponds nearby area. In this study, four bio-treatments were applied for the in-situ bioremediation and valorization of OMW sludge: Landfarming, phytoremediation, composting and vermicomposting. In all cases, the OMW sludge was added with organic residues (mushroom compost, rabbit manure, and chicken manure). The bio-treatments were carried out in duplicate, inoculated and non-inoculated, to determine the effect of a specialized fungal consortium (Aspergillus ochraceus H2 and Scedosporium apiospermum H16) on the efficacy of the bio-treatments. The evaluation of chemical parameters, toxicity, and functional microbial biodiversity revealed that the four techniques depleted the toxicity and favored the stimulation of functional microbiota. Landfarming and phytoremediation allowed the decontamination and improvement of soils. Composting and vermicomposting also offered high-quality products of agronomic interest. Inoculation improved the bioremediation effectiveness. Biological treatments are effective for the safe recovery of contaminated OMW sludge into high-quality services and products.

Diversity of rhizospheric and endophytic bacteria isolated from dried fruit of Ficus carica

There is currently an increasing demand for the characterization of endophytic bacteria isolated from different parts of plants (rhizosphere, roots, fruit, leaf) in order to improve the organic agriculture practices. The current research was performed to identify both rhizospheric bacteria isolated from the rhizosphere of Ficus carica in three different sites in the north of Tunisia and endophytic bacteria isolated from dried figs. We then characterized them for a diversity of plant growth-promoting (PGP) activities. A collection of 120 isolates from rhizospheric soil and 9 isolates from dried figs was obtained and purified. 16SrDNA gene amplification of rhizospheric bacteria revealed significant diversity and allowed for the assigning of the isolates to 6 phyla: Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Representative strains of the collection (90 strains) were tested for numerous PGP activities and resistance to abiotic stresses. The most common PGP trait for all bacteria from the three regions was siderophore production (62%), followed by cellulase (38%), then protease activity (37%), then by lipases activity (17%) and lastly by solubilization of phosphates (9%). Twenty -three strains that showed most PGP traits were selected, 8 strains presented 12 or more, and 15 strains displayed between 7 and 11 of 17 PGP activities. The majority of the isolates manifested a possible adaptation to abiotic stress and unfavorable environments. PCR-DGGE analysis of soil rhizosphere of the three sites allowed also for the acquisition of a Cluster analysis of rhizospheric bacterial communities. Our current study identified and characterized for the first time in Tunisia rhizospheric and endophytic bacteria from dried fruit of Ficus carica.

Driving factors of nitrogen conversion during chicken manure aerobic composting under penicillin G residue: Quorum sensing and its signaling molecules

This study explored effects of different concentrations of penicillin G on nitrogen conversion, bacterial community composition, and quorum sensing during chicken manure aerobic composting. After composting, adding penicillin G down-regulated the abundance of 71 genera and up-regulated the abundance of 103 genera. These bacterial genera were mainly Firmicutes and Proteobacteria. 16S rRNA gene sequencing was employed for function prediction, and the results showed that the addition of penicillin G increased nitrification, reduced denitrification. The autoinducer-1 (AI-1), autoinducer-3 (AI-3) and Phr signal molecules further participated in the nitrogen cycle by regulating the population behavior among multiple bacterial genera. In addition, SEM analysis showed that the quorum sensing system negatively regulated the abundance of genus related to the nitrogen conversion during chicken manure aerobic composting. This is a new theoretical analysis of the research on the treatment of hazardous materials.

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.

Olive Mill and Olive Pomace Evaporation Pond’s By-Products: Toxic Level Determination and Role of Indigenous Microbiota in Toxicity Alleviation

Diverse vegetable oils are extracted from oleagenic trees and plants all over the world. In particular, olive oil represents a strategic socio-economic branch in the Mediterranean countries. These countries use either two or three-phase olive oil extraction systems. In this work, we focus on the by-products from three-phase olive oil extraction, which are the liquid olive mill wastewater (OMW) and the solid olive mill pomace (OMP) rejected in evaporative ponds. The disposal of this recalcitrant waste poses environmental problems such as the death of different species of insects and animals. In-depth ICP-OES analysis of the heavy metal composition of OMW and OMP revealed the presence of many metals ranging from non-toxic to highly toxic. The LC-HRMS characterization of these by-products indicated the presence of several secondary metabolites harmful to humans or to the environment. Thus, we aimed to identify OMW and OMP indigenous microbiota through metagenomics. The bacterial population was dominated by the Acetobacter (49.7%), Gluconobacter (17.3%), Gortzia (13.7%) and Nardonalla (5.3%) genera. The most abundant fungal genera were Nakazawaea, Saccharomyces, Lachancea and Candida. These microbial genera are responsible for OMW, OMP and soil toxicity alleviation.

Bio-hydrolysis of used soybean oil: environmental-friendly technology using microbial consortium

In this work, strains of Bacillus subtilis were inoculated in consortium with Rhodotorula mucilaginosa into spent soy oil as aiming to biological treatment and low-cost reuse. The microorganisms were previously isolated and selected for the lipolytic capacity of the alperujo residue generated during the processing of olive oil. For fermentation, bioassays containing Rhodotorula mucilaginosa isolated from alperujo and Candida rugosa CCMA 00371, both co-inoculated with Bacillus subtilis CCMA 0085 in medium containing (% w/v) 0.075 glucose and 0.375 (NH₄)₃ PO₄ in 75 mL of water and 75 mL of spent soy oil. Despite the low biomass productivity, it has favorable characteristics to be used in animal feed supplementation. Spent soy oil was used as a carbon source proven by Bartha respirometer. The strains of R. mucilaginosa UFLA RAS 144 and B. subtilis CCMA 0085 are promising inoculants for oil degradation and can be applied in a waste treatment system.

Milk yield of cows submitted to different levels of olive pomace in the diet

The cultivation of olive trees is expanding in Brazil, mainly in Rio Grande do Sul in order to meet the demand for olive oil, the main product of the industrialization of olives. However, from the extraction, there is a significant generation of waste. This residue has high moisture and an appropriate destination is necessary given its environmental and economic importance. The chemical composition of the residue is similar to other products used in animal feed, such as corn silage or sorghum, in relation to DM, CP and NDF, the differential being high levels of EE and ADL. In order to evaluate the replacement of corn silage by the extraction residue of olive oil (olive pomace), eight Holstein dairy cow, between 90 and 100 days of lactation, were used, making a double Latin square (4x4). Analyzes were made regarding animals, feed and milk product in order to verify the feasibility of the substitution. The inclusion of olive pomace, conserved as silage, to replace corn silage, in the diet of lactating cows up to 15% (dry basis) does not alter milk production, as well as its composition and feed efficiency.

Succession of the bacterial community structure and functional prediction in two composting systems viewed through metatranscriptomics

In this work, Illumina MiSeq sequencing of cDNA from metatranscriptomics RNA reverse transcription were employed in combination with phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) to estimate the dynamic variations of bacterial community structures and metabolic functions in a bioreactor and traditional composting process. Results showed that the change of bacterial α-diversity in the first three stages exhibit opposite trends in the two composting systems. The four most abundant phyla were the same in both systems (Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria), but the most abundant genera were different. The five most abundant genus-level groups in the bioreactor were Psychrobacter, Galbibacter, Pseudomonas, Staphylococcus and Flavobacterium. Within the same phase, the functional bacteria were dramatically different in the two composting processes. In the bioreactor system both bacterial community structure and metabolism function were greatly affected by available phosphorus.

Molecular mechanisms underlying lignocellulose degradation and antibiotic resistance genes removal revealed via metagenomics analysis during different agricultural wastes composting

In this study, the differences on the physico-chemical parameters, lignocellulose degradation, dynamic succession of microbial community, gene expression of carbohydrate-active enzymes and antibiotics resistance genes were compared during composting systems of bagasse pith/pig manure (BP) and manioc waste/pig manure (MW). The results revealed that biodegradation rates of organic matter, cellulose, hemicellulose and lignin (29.14%, 17.53%,45.36% and 36.48%) in BP were higher than those (15.59%, 16.74%, 41.23% and 29.77%) in MW. In addition, the relative abundance of Bacillus, Luteimonas, Clostridium, Pseudomonas, Streptomyces and expression of genes encoding carbohydrate- active enzymes in BP were higher than those in MW based on metagenomics sequencing. During composting, antibiotics and antibiotic resistance genes were substantially reduced, but the removal efficiency was divergent in the both samples. Taken together, metagenomics analysis was a potential method for evaluating lignocellulose's biodegradation process and determining the elimination of antibiotic and antibiotic resistance genes from different composting sources of biomass.

A compost-derived thermophilic microbial consortium enhances the humification process and alters the microbial diversity during composting

This work was conducted to assess the influence of a compost-born multifunctional thermophilic microbial consortium (CTMC) on the physico-chemical parameters, organic matter (OM) transformation and dynamic succession of microbial communities in dairy manure-sugarcane leaves co-composting. The results revealed that CTMC inoculation not only improved the bio-degradation of OM and lignocellulose but also distinctly enhanced the aromaticity and stability degrees of dissolved organic matter and humic substance (HS). Additionally, the complexity and diversity of bacterial and fungal community increased after inoculation. Redundancy analysis indicated that the microbial communities compositions and the physico-chemical parameters interacted with each other in humification process. The dominated bacterial and fungal species related to lignocellulose degradation and humification process were also detected. Accordingly, this research could put forward a possible optimized inoculation strategy to enhance the mineralization of organic carbon, accelerate the lignocellulose degradation and promote the humification process in solid organic waste composting.

Effects of biochar amendment on bacterial and fungal diversity for co-composting of gelatin industry sludge mixed with organic fraction of municipal solid waste

The aim of the study was to evaluate the bacterial and fungal diversities of 18contrastivecomposts applied with 17 different sources mad biochars applied treatments using 16S rRNA and 18S rDNA technology, while T-1 used as a control. The results showed that bacterial species of the phyla Actinobacteria, Proteobacteria and Chloroflexi, and fungi of the phylum Ascomycota and Basidiomycota were pre-dominant among the all treatments. The bacterial genus Subgroup_6_norank, Nocardioides, Pseudonocardia, Sphingomonas, Solirubrobacter and RB41_norank are first time identified in composting ecosystem. In addition, the fungal genus Ascomycota_unclassified, Aspergillus, Penicillium, Pleosporales_unclassified and Herpotrichlellacease_unclassified ubiquitous among the all compost. The Shannon and refraction-curve biodiversity indices showed a clear heterogeneity among all the treatments, which could be due to isolation of new genera in this system. Finally, the principal component analysis of the relative number of sequences also confirmed that bacterial and fungal population indiscriminate in different sources mad biochar applied treatments.

Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics

Composting is a promising source of new organisms and thermostable enzymes that may be helpful in environmental management and industrial processes. Here we present results of metagenomic- and metatranscriptomic-based analyses of a large composting operation in the São Paulo Zoo Park. This composting exhibits a sustained thermophilic profile (50 °C to 75 °C), which seems to preclude fungal activity. The main novelty of our study is the combination of time-series sampling with shotgun DNA, 16S rRNA gene amplicon, and metatranscriptome high-throughput sequencing, enabling an unprecedented detailed view of microbial community structure, dynamics, and function in this ecosystem. The time-series data showed that the turning procedure has a strong impact on the compost microbiota, restoring to a certain extent the population profile seen at the beginning of the process; and that lignocellulosic biomass deconstruction occurs synergistically and sequentially, with hemicellulose being degraded preferentially to cellulose and lignin. Moreover, our sequencing data allowed near-complete genome reconstruction of five bacterial species previously found in biomass-degrading environments and of a novel biodegrading bacterial species, likely a new genus in the order Bacillales. The data and analyses provided are a rich source for additional investigations of thermophilic composting microbiology.

Responses of Aquatic Bacteria to Terrestrial Runoff: Effects on Community Structure and Key Taxonomic Groups

Organic fertilizer application is often touted as an economical and effective method to increase soil fertility. However, this amendment may increase dissolved organic carbon (DOC) runoff into downstream aquatic ecosystems and may consequently alter aquatic microbial community. We focused on understanding the effects of DOC runoff from soils amended with compost, vermicompost, or biochar on the aquatic microbial community of a tropical reservoir. Runoff collected from a series of rainfall simulations on soils amended with different organic fertilizers was incubated for 16 days in a series of 200 L mesocosms filled with water from a downstream reservoir. We applied 454 high throughput pyrosequencing for bacterial 16S rRNA genes to analyze microbial communities. After 16 days of incubation, the richness and evenness of the microbial communities present decreased in the mesocosms amended with any organic fertilizers, except for the evenness in the mesocosms amended with compost runoff. In contrast, they increased in the reservoir water control and soil-only amended mesocosms. Community structure was mainly affected by pH and DOC concentration. Compared to the autochthonous organic carbon produced during primary production, the addition of allochthonous DOC from these organic amendments seemed to exert a stronger effect on the communities over the period of incubation. While the Proteobacteria and Actinobacteria classes were positively associated with higher DOC concentration, the number of sequences representing key bacterial groups differed between mesocosms particularly between the biochar runoff addition and the compost or vermi-compost runoff additions. The genera of Propionibacterium spp. and Methylobacterium spp. were highly abundant in the compost runoff additions suggesting that they may represent sentinel species of complex organic carbon inputs. Overall, this work further underlines the importance of studying the off-site impacts of organic fertilizers as their impact on downstream aquatic systems is not negligible.

Characterization of the Skin Microbiota in Italian Stream Frogs (Rana italica) Infected and Uninfected by a Cutaneous Parasitic Disease

In human and wildlife populations, the natural microbiota plays an important role in health maintenance and the prevention of emerging infectious diseases. In amphibians, infectious diseases have been closely associated with population decline and extinction worldwide. Skin symbiont communities have been suggested as one of the factors driving the different susceptibilities of amphibians to diseases. The activity of the skin microbiota of amphibians against fungal pathogens, such as Batrachochytrium dendrobatidis, has been examined extensively, whereas its protective role towards the cutaneous infectious diseases caused by Amphibiocystidium parasites has not yet been elucidated in detail. In the present study, we investigated, for the first time, the cutaneous microbiota of the Italian stream frog (Rana italica) and characterized the microbial assemblages of frogs uninfected and infected by Amphibiocystidium using the Illumina next-generation sequencing of 16S rRNA gene fragments. A total of 629 different OTUs belonging to 16 different phyla were detected. Bacterial populations shared by all individuals represented only one fifth of all OTUs and were dominated by a small number of OTUs. Statistical analyses based on Bray-Curtis distances showed that uninfected and infected specimens had distinct cutaneous bacterial community structures. Phylotypes belonging to the genera Janthinobacterium, Pseudomonas, and Flavobacterium were more abundant, and sometimes almost exclusively present, in uninfected than in infected specimens. These bacterial populations, known to exhibit antifungal activity in amphibians, may also play a role in protection against cutaneous infectious diseases caused by Amphibiocystidium parasites.

Pyrosequencing reveals bacterial community differences in composting and vermicomposting on the stabilization of mixed sewage sludge and cattle dung

This study aimed to compare the microbial community structures and compositions in composting and vermicomposting processes. We applied 454 high-throughput pyrosequencing to analyze the 16S rRNA gene of bacteria obtained from bio-stabilization of sewage sludge and cattle dung. Results demonstrated that vermicomposting process presented higher operational taxonomic units and bacterial diversity than the composting. Analysis using weighted UniFrac indicated that composting exhibited higher effects on shaping microbial community structure than the vermicomposting. The succession of dominant bacteria was also detected during composting. Firmicutes was the dominant bacteria in the thermophilic phase of composting and shifted to Actinomycetes in the maturing stage. By contrast, Proteobacteria accounted for the highest proportions in the whole process of the vermicomposting. Furthermore, vermicomposting contained more uncultured and unidentified bacteria at the taxonomy level of genus than the composting. In summary, the bacterial community during composting significantly differed from that during vermicomposting. These two techniques played different roles in changing the diversity and composition of microbial communities.

Enhanced short chain fatty acids production from waste activated sludge conditioning with typical agricultural residues: carbon source composition regulates community functions

BACKGROUND

A wide range of value-added by-products can be potentially produced from waste activated sludge (WAS) through anaerobic fermentation, among which short-chain fatty acids (SCFAs) are versatile green chemicals, but the conversion yield of SCFAs is usually constrained by the low carbon-to-nitrogen ratio of the original WAS. Conditioning of the WAS with cellulose-containing agricultural residues (ARs) has been reported to be an efficient and economical solution for balancing its nutrient components. However, contributions of different ARs to SCFAs production are still not well understood.

RESULTS

To optimize SCFAs production through carbon conditioning of WAS, we investigated the effects of two typical ARs [straws and spent mushroom substrates (SMSs)] on WAS hydrolysis and acidification in semi-continuous anaerobic fermentation. Straw-conditioning group showed a threefold increase in short-chain fatty acids yield over blank test (without conditioning), which was 1.2-fold higher than that yielded by SMS-conditioning. The maximum SCFAs yield in straw-conditioning groups reached 486.6 mgCOD/gVSS (Sludge retention time of 8 d) and the highest volumetric SCFAs productivity was 1.83 kgCOD/([Formula: see text]) (Sludge retention time of 5 d). In batch WAS fermentation tests, higher initial SCFAs production rates were achieved in straw-conditioning groups [49.5 and 52.2 mgCOD/(L·h)] than SMS-conditioning groups [41.5 and 35.2 mgCOD/(L·h)]. High-throughput sequencing analysis revealed that the microbial communities were significantly shifted in two conditioning systems. Carbohydrate-fermentation-related genera (such as Clostridium IV, Xylanibacter, and Parabacteroides) and protein-fermentation-related genus Lysinibacillus were enriched by straw-conditioning, while totally different fermentation genera (Levilinea, Proteiniphilum, and Petrimonas) were enriched by SMS-conditioning. Canonical correlation analysis illustrated that the enrichment of characteristic genera in straw-conditioning group showed positive correlation with the content of cellulose and hemicellulose, but showed negative correlation with the content of lignin and humus.

CONCLUSIONS

Compared with SMSs, straw-conditioning remarkably accelerated WAS hydrolysis and conversion, resulting in higher SCFAs yield. Distinct microbial communities were induced by different types of ARs. And the communities induced by straw-conditioning were verified with better acid production ability than SMS-conditioning. High cellulose accessibility of carbohydrate substrates played a crucial role in enriching bacteria with better hydrolysis and acidification abilities.

Enzymatic characterization of microbial isolates from lignocellulose waste composting: chronological evolution

Successful composting is dependent upon microbial performance. An interdependent relationship is established between environmental and nutritional properties that rule the process and characteristics of the dominant microbial communities. To reach a better understanding of this relationship, the dynamics of major metabolic activities associated with cultivable isolates according to composting phases were evaluated. Ammonification (72.04%), amylolysis (35.65%), hemicellulolyis (30.75%), and proteolysis (33.61%) were the more frequent activities among isolates, with mesophilic bacteria and fungi as the prevalent microbial communities. Bacteria were mainly responsible for starch hydrolysis, while a higher percentage of hemicellulolytic and proteolytic isolates were ascribable to fungi. Composting seems to exert a functional selective effect on microbial communities by promoting the presence of specific metabolically dominant groups at each stage of the process. Moreover, the application of conglomerate analysis led to the statement of a clear correlation between the chronology of the process and characteristics of the associated microbiota. According to metabolic capabilities of the isolates and their density, three clear clusters were obtained corresponding to the start of the process, including the first thermophilic peak, the rest of the bio-oxidative stage, and the maturation phase.

Exploiting composting biodiversity: study of the persistent and biotechnologically relevant microorganisms from lignocellulose-based composting

The composting ecosystem is a suitable source for the discovery of novel microorganisms and secondary metabolites. This work analyzes the identity of microbial community that persists throughout lignocellulose-based composting, evaluates their metabolic activities and studies the capability of selected isolates for composting bioaugmentation. Bacterial species of the phyla Firmicutes, Actinobacteria and Proteobacteria and fungi of the phylum Ascomycota were ubiquitous throughout the composting. The species Arthrobacter russicus, Microbacterium gubbeenense, Ochrocladosporium frigidarii and Cladosporium lignicola are detected for the first time in this ecosystem. In addition, several bacterial and fungal isolates exhibited a wide range of metabolic capabilities such as polymers (lignocellulose, protein, lipids, pectin and starch) breakdown and phosphate-solubilization that may find many biotechnological applications. In particular, Streptomyces albus BM292, Gibellulopsis nigrescens FM1397 and FM1411, Bacillus licheniformis BT575, Bacillus smithii AT907 and Alternaria tenuissima FM1385 exhibited a great potential as inoculants for composting bioaugmentation.

Biorefinery based on olive biomass. State of the art and future trends

With currently more than nine million hectares, olive tree cultivation has spread worldwide, table olives and olive oil as the main products. Moreover, a number of by-products and residues derived from both tree cultivation and the process of industrial olive oil production, most having no practical applications, are obtained yearly. This paper reviews the research regarding these by-products, namely biomass from olive tree pruning, olive stones, olive pomace and wastewaters obtained from the process of olive oil production. Furthermore, a wide range of compounds has been identified and can be produced using a broad definition of the term biorefinery based on olive tree biomass. As an example, this paper reviews ethanol production as one of the main proposed applications, as well as research on other value-added products. Finally, this paper also assesses recent technological advances, future perspectives and challenges in each stage of the process.

The microbiology of olive mill wastes

Olive mill wastes (OMWs) are high-strength organic effluents, which upon disposal can degrade soil and water quality, negatively affecting aquatic and terrestrial ecosystems. The main purpose of this review paper is to provide an up-to-date knowledge concerning the microbial communities identified over the past 20 years in olive mill wastes using both culture-dependent and independent approaches. A database survey of 16S rRNA gene sequences (585 records in total) obtained from olive mill waste environments revealed the dominance of members of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria. Independent studies confirmed that OMW microbial communities' structure is cultivar dependent. On the other hand, the detection of fecal bacteria and other potential human pathogens in OMWs is of major concern and deserves further examination. Despite the fact that the degradation and detoxification of the olive mill wastes have been mostly investigated through the application of known bacterial and fungal species originated from other environmental sources, the biotechnological potential of indigenous microbiota should be further exploited in respect to olive mill waste bioremediation and inactivation of plant and human pathogens. The implementation of omic and metagenomic approaches will further elucidate disposal issues of olive mill wastes.

Microbially-enhanced composting of olive mill solid waste (wet husk): bacterial and fungal community dynamics at industrial pilot and farm level

Bacterial and fungal community dynamics during microbially-enhanced composting of olive mill solid waste (wet husk), used as a sole raw material, were analysed in a process carried out at industrial pilot and at farm level by the PCR-DGGE profiling of the 16 and 26S rRNA genes. The use of microbial starters enhanced the biotransformation process leading to an earlier and increased level of bacterial diversity. The bacterial community showed a change within 15 days during the first phases of composting. Without microbial starters bacterial biodiversity increased within 60 days. Moreover, the thermophilic phase was characterized by the highest bacterial biodiversity. By contrast, the biodiversity of fungal communities in the piles composted with the starters decreased during the thermophilic phase. The biodiversity of the microbial populations, along with physico-chemical traits, evolved similarly at industrial pilot and farm level, showing different maturation times.

Isolation and Identification of High Efficient Oil-Degrading Bacteria and Formulation of Complex Bacteria

In this experiment, 25 oil degrading bacteria strains were isolated from the beach near Dalian Bay. The top 4 high efficient oil-degrading bacteria（SQ、SY 、SW、SC） were selected to be studied. Using Physiological and biochemical identification, electron microscopy, and 16S rDNA sequence analysis, strain SQ was identified as Advenella kashmirensis，SY was identified as Achromobacter xylosoxidans, SW was identified as Acinetobacter venetianus，SC was identified as Alcaligenes xylosoxidans subsp.xylosoxidans. For the first time this experiment provided reference to application and degradation characteristics of Advenella kashmirensis in crude oil treatment. These four marine oil degrading bacteria were selected to form bacterial consortium. The most efficient mixed strains were constructed by using these four strains with proportional combination. The oil removal ratio of the optimal mixed strains increased to 70.33%, nearly 25% higher than the highest degradation rate of single bacterium, showing significant synergism in the bacterial consortium. Advenella kashmirensis enhanced oil degradation obviously, playing a crucial role in the bacterial consortium.