Editorial for Special Issue "Unleashing the Hidden Potential of Anaerobic Fungi".

Anaerobic fungi (AF) of the phylum are a very peculiar group of microorganisms [...

Effect of Growth Media on the Diversity of from Non-Rumen Habitats.

Anaerobic fungi (AF), belonging to the phylum are a pivotal component of the digestive tract microbiome of various herbivorous animals. In the last decade, the diversity of AF has rapidly expanded due to the exploration of numerous (novel) habitats. Studies aiming at understanding the role of AF require robust and reliable isolation and cultivation techniques, many of which remained unchanged for decades.

Simultaneous Metabarcoding and Quantification of from Environmental Samples: Insights into Community Composition and Novel Lineages.

Anaerobic fungi from the herbivore digestive tract () are primary lignocellulose modifiers and hold promise for biotechnological applications. Their molecular detection is currently difficult due to the non-specificity of published primer pairs, which impairs evolutionary and ecological research with environmental samples. We developed and validated a -specific PCR primer pair targeting the D2 region of the ribosomal large subunit suitable for screening, quantifying, and sequencing.

Uncovering antimicrobial resistance in three agricultural biogas plants using plant-based substrates.

Antimicrobial resistance (AMR) is becoming an increasing global concern and the anaerobic digestion (AD) process represents a potential transmission route when digestates are used as fertilizing agents. AMR contaminants, e.g.

Effects of CO enrichment on the anaerobic digestion of sewage sludge in continuously operated fermenters.

The effect of CO enrichment in sewage sludge anaerobic digestion (AD) as a potential strategy to improve the biogas yield was assessed at increasing organic loading rates (OLR). Effects on process performance and resilience were evaluated in long-term continuous AD experiments at lab-scale. The specific methane production (SMP) was sustainably enhanced in the test digester compared to a control at elevated OLRs, reaching an increase of 6 ± 12% on average at the highest OLR tested (4.

gen. nov, sp. nov., the First Cultured Representative of the Uncultured SK4 Clade from Aoudad Sheep and Alpaca.

We report on the isolation of the previously-uncultured SK4 lineage, by two independent research groups, from a wild aoudad sheep rumen sample (Texas, USA) and an alpaca fecal sample (Baden-Württemberg, Germany). Isolates from both locations showed near-identical morphological and microscopic features, forming medium-sized (2-5 mm) white filamentous colonies with a white center of sporangia, on agar roll tubes and a heavy biofilm in liquid media. Microscopic analysis revealed monocentric thalli, and spherical polyflagellated zoospores with 7-20 flagella.

Importance of for Hydrolytic Biomass Degradation in Co-Culture with .

Bacterial hydrolysis of polysaccharides is an important step for the production of sustainable energy, for example during the conversion of plant biomass to methane-rich biogas. Previously, was identified as cellulolytic key player in thermophilic biogas microbiomes with a great frequency as an accompanying organism. The aim of this study was to physiologically characterize a recently isolated co-culture of and the saccharolytic bacterium from a laboratory-scale biogas fermenter.

Load change capability of an anaerobic thermophilic trickle bed reactor for dynamic H/CO biomethanation.

Increasing shares of energy production originating from fluctuating renewable sources require measures that are able to balance power production for a stable electricity grid. H/CO biomethanation is a suitable approach to convert fluctuating excess renewable energy into the storable substitute natural gas. This study investigated the rapid load change capability of an anaerobic thermophilic trickle bed reactor while maintaining a high methane content.

Isolation, identification and characterization of lignocellulolytic aerobic and anaerobic fungi in one- and two-phase biogas plants.

Aerobic and anaerobic fungi are among the most effective plant biomass degraders known and have high potential to increase the efficiency of lignocellulosic biomass utilization, such as for biogas generation. However, limited information is available on their contribution to such industrial processes. Therefore, the presence of fungi along the biogas production chain of one-phase and two-phase biogas plants in Germany was analyzed.

Accelerated biogas production from lignocellulosic biomass after pre-treatment with Neocallimastix frontalis.

Two Neocallimastix frontalis strains, isolated from rumen fluid of a cow and of a chamois, were assessed for their ability to degrade lignocellulosic biomass. Two independent batch experiments were performed. Each experiment was split into two phases: hydrolysis phase and batch fermentation phase.

High performance biological methanation in a thermophilic anaerobic trickle bed reactor.

In order to enhance energy efficiency of biological methanation of CO and H, this study investigated the performance of a thermophilic (55°C) anaerobic trickle bed reactor (ATBR) (58.1L) at ambient pressure. With a methane production rate of up to 15.

Presence and transcriptional activity of anaerobic fungi in agricultural biogas plants.

Bioaugmentation with anaerobic fungi (AF) is promising for improved biogas generation from lignocelluloses-rich substrates. However, before implementing AF into biogas processes it is necessary to investigate their natural occurrence, community structure and transcriptional activity in agricultural biogas plants. Thus, AF were detected with three specific PCR based methods: (i) Copies of their 18S genes were found in 7 of 10 biogas plants.

Influence of nitrogen-rich substrates on biogas production and on the methanogenic community under mesophilic and thermophilic conditions.

Grass silage was evaluated as a possible substrate in anaerobic digestion for generation of biogas in mesophilic and thermophilic long-term operation. Furthermore, the molecular biological parameter Metabolic Quotient (MQ) was evaluated as early warning system to predict process disturbance. Since this substrate is rich in nitrogen, high ammonia concentration of up to 2.

Development of three specific PCR-based tools to determine quantity, cellulolytic transcriptional activity and phylogeny of anaerobic fungi.

Anaerobic fungi (AF) decompose plant material with their rhizoid and multiple cellulolytic enzymes. They disintegrate the complex structure of lignocellulosic substrates, making them more accessible and suitable for further microbial degradation. There is also much interest in their use as biocatalysts for biotechnological applications.

DNA and RNA Extraction and Quantitative Real-Time PCR-Based Assays for Biogas Biocenoses in an Interlaboratory Comparison.

Five institutional partners participated in an interlaboratory comparison of nucleic acid extraction, RNA preservation and quantitative Real-Time PCR (qPCR) based assays for biogas biocenoses derived from different grass silage digesting laboratory and pilot scale fermenters. A kit format DNA extraction system based on physical and chemical lysis with excellent extraction efficiency yielded highly reproducible results among the partners and clearly outperformed a traditional CTAB/chloroform/isoamylalcohol based method. Analytical purpose, sample texture, consistency and upstream pretreatment steps determine the modifications that should be applied to achieve maximum efficiency in the trade-off between extract purity and nucleic acid recovery rate.

Hygiene and Sanitation in Biogas Plants.

The increasing number of agricultural biogas plants and higher amounts of digestate spread on agricultural land arouse a considerable interest in the hygiene situation of digested products. This chapter reviews the current knowledge on sanitation during anaerobic digestion and the hygienic status of digestate concerning a multitude of pathogens potentially compromising the health of humans, animals and plants. Physical, chemical and biological parameters influencing the efficiency of sanitation in anaerobic digestion are considered.

Microbiology and Molecular Biology Tools for Biogas Process Analysis, Diagnosis and Control.

Many biotechnological processes such as biogas production or defined biotransformations are carried out by microorganisms or tightly cooperating microbial communities. Process breakdown is the maximum credible accident for the operator. Any time savings that can be provided by suitable early-warning systems and allow for specific countermeasures are of great value.

Towards molecular biomarkers for biogas production from lignocellulose-rich substrates.

Biogas production from lignocellulose-rich agricultural residues is gaining increasingly importance in sustainable energy production. Hydrolysis/acidogenesis (H/A) of lignocellulose as the initial rate-limiting step deserves particular optimization. A mixture of straw/hay was methanized applying two-phase digester systems with an initial H/A reactor and a one-stage system at different, meso- and thermophilic temperatures.

Process diagnosis using methanogenic Archaea in maize-fed, trace element depleted fermenters.

A mesophilic maize-fed pilot-scale fermenter was severely acidified due to trace element (TE) deficiency. Mainly cobalt (0.07 mg * kg(-1) fresh mass (FM)), selenium (0.

Assessment of the viability of Cryptosporidium parvum oocysts with the induction ratio of hsp70 mRNA production in manure.

Determining the presence of viable Cryptosporidium parvum oocysts in complex environmental matrices in hygiene control can prevent the contamination of water resources and food with this pathogen. This study assessed the induction ratio of hsp70 mRNA production by heat shock in different oocysts as a marker of viability. Using different procedures for (m)RNA extraction directly from manure and reverse transcription real-time qPCR, this study found slightly increased hsp70 mRNA contents in viable oocysts that were heat shock induced at 45°C for 20 min compared to not induced oocysts (1.

Evaluation of two methods for quantification of hsp70 mRNA from the waterborne pathogen Cryptosporidium parvum by reverse transcription real-time PCR in environmental samples.

We optimized and evaluated two mRNA extraction methods to quantify induced hsp70 mRNA from viable and injured Cryptosporidium parvum oocysts by reverse transcription quantitative real-time PCR (RT-qPCR) in raw and treated manure. Methods based on guanidinium isothiocyanate/phenol/chloroform (GITC-PC) purification and direct mRNA extraction with magnetic oligo(dT)25-coated beads were evaluated for applicability and sensitivity. Both methods proved to be suitable for processing manure samples.

Ochrobactrum oryzae sp. nov., an endophytic bacterial species isolated from deep-water rice in India.

A non-pigmented, motile, Gram-negative bacterium designated MTCC 4195(T) was isolated from surface-sterilized seeds and plant tissue from deep-water rice (Oryza sativa) cultivated in Suraha Tal Lake in northern India. This isolate was shown to reinfect and colonize deep-water rice endophytically. The highest level of 16S rRNA sequence similarity (96.

Genetic and phenotypic microdiversity of Ochrobactrum spp.

The diversity of Ochrobactrum anthropi, Ochrobactrum intermedium, Ochrobactrum tritici and Ochrobactrum grignonense in agricultural soil and on the wheat rhizoplane was investigated. O. anthropi was isolated both from soil and from the rhizoplane, O.

Comparative sequence analysis of the internal transcribed spacer 1 of Ochrobactrum species.

The internal 16S/23S rDNA (rrs/rrl) internal spacer region 1 (ITS1) of 54 Ochrobactrum strains and close relatives was analysed. Separation of ITS1 containing PCR products by gel-electrophoresis, DGGE, cloning and sequencing revealed ITS1 length and sequence heterogeneity. We found up to 5 different allelic ITS1 stretches within a single strain (Ochrobactrum intermedium LMG 3301T), and 2-3 different ITS1 alleles in O.