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.

No time to die: Comparative study on preservation protocols for anaerobic fungi.

Anaerobic fungi (AF, phylum Neocallimastigomycota) are best known for their ability to anaerobically degrade recalcitrant lignocellulosic biomass through mechanic and enzymatic means. While their biotechnological potential is well-recognized, applied research on AF is still hampered by the time-consuming and cost-intensive laboratory routines required to isolate, maintain, and preserve AF cultures. Reliable long-term preservation of specific AF strains would aid basic as well as applied research, but commonly used laboratory protocols for AF preservation can show erratic survival rates and usually exhibit only moderate resuscitation success for up to one or two years after preservation.

Why eDNA fractions need consideration in biomonitoring.

The analysis of environmental DNA (eDNA) is revolutionizing the monitoring of biodiversity as it allows to assess organismic diversity at large scale and unprecedented taxonomic detail. However, eDNA consists of an extracellular and intracellular fraction, each characterized by particular properties that determine the retrievable information on when and where organisms live or have been living. Here, we review the fractions of eDNA, describe how to obtain them from environmental samples and present a four-scenario concept that aims at enhancing spatial and temporal resolution of eDNA-based monitoring.

Microbial response on the first full-scale DEMON® biomass transfer for mainstream deammonification.

Sidestream partial nitritation and deammonification (pN/A) of high-strength ammonia wastewater is a well-established technology. Its expansion to the mainstream is, however mainly impeded by poor retention of anaerobic ammonia oxidizing bacteria (AnAOB), insufficient repression of nitrite oxidizing bacteria (NOB) and difficult control of soluble chemical oxygen demand and nitrite levels. At the municipal wastewater treatment plant in Strass (Austria) the microbial consortium was exhaustively monitored at full-scale over one and a half year with regular transfer of sidestream DEMON® biomass and further retention and enrichment of granular anammox biomass via hydrocyclone operation.

CoMA - an intuitive and user-friendly pipeline for amplicon-sequencing data analysis.

In recent years, there has been a veritable boost in next-generation sequencing (NGS) of gene amplicons in biological and medical studies. Huge amounts of data are produced and need to be analyzed adequately. Various online and offline analysis tools are available; however, most of them require extensive expertise in computer science or bioinformatics, and often a Linux-based operating system.

The masking effect of extracellular DNA and robustness of intracellular DNA in anaerobic digester NGS studies: A discriminatory study of the total DNA pool.

Most commonly, next generation sequencing-based microbiome studies are performed on the total DNA (totDNA) pool; however, this consists of extracellular- (exDNA) and intracellular (iDNA) DNA fractions. By investigating the microbiomes of different anaerobic digesters over time, we found that totDNA suggested lower species richness considering all and/or only common species and yielded fewer unique reads as compared to iDNA. Additionally, exDNA-derived sequences were more similar to those from totDNA than from iDNA and, finally, iDNA showed the best performance in tracking temporal changes in microbial communities.

Quantities of Intra- and Extracellular DNA Reveal Information About Activity and Physiological State of Methanogenic Archaea.

Although being a common aim of many microbial ecology studies, measuring individual physiological conditions of a microbial group or species within a complex consortium is still a challenge. Here, we propose a novel approach that is based on the quantification of sequentially extracted extracellular (exDNA) and intracellular DNA (iDNA) and reveals information about cell lysis and activity of methanogenic archaea within a biogas-producing microbial community. We monitored the methane production rates of differently treated batch anaerobic cultures and compared the concentrations of the alpha subunit of the methyl coenzyme M reductase gene of methanogenic archaea in extracellular and intracellular DNA fractions and in the classically extracted total DNA pool.

Employing anaerobic fungi in biogas production: challenges & opportunities.

Anaerobic fungi (AF, phylum Neocallimastigomycota) are best known for their ability to efficiently break down lignocellulosic biomass. Their unique combination of mechanical and enzymatic attacks on recalcitrant plant structures bears great potential for enhancement of the anaerobic digestion (AD) process. Although scientists in this field have long agreed upon the potential of AF for biotechnology, research is only recently gaining traction.

Biomethanation at 45 °C offers high process efficiency and supports hygienisation.

The aim of this work was to prove a process temperature of 45 °C as a practical alternative to commonly applied mesophilic (37 °C) and thermophilic (55 °C) anaerobic digestion (AD). Regarding methane production, no differences were found between the three temperature regimes. However, the maximum possible loading rate at 45 °C exceeded that at 37 °C and 55 °C.

Simple yet effective: Microbial and biotechnological benefits of rumen liquid addition to lignocellulose-degrading biogas plants.

In biogas plants, lignocellulose-rich biomass (LCB) is particularly slowly degraded, causing high hydraulic retention times. This fact lowers the interests for such substrates. To enhance LCB-degradation, cattle rumen fluid, a highly active microbial resource accruing in the growing meat industry, might be used as a potential source for bioaugmentation.

Temperature shapes the microbiota in anaerobic digestion and drives efficiency to a maximum at 45 °C.

Throwing longstanding habits over the pile may be necessary to improve biogas production, in particular when it comes to the process temperature. Its effect on biogas production was investigated with lab-scale reactors operated in fed-batch mode (cattle slurry and maize straw) at 10-55 °C over six months. Biochemical and microbial changes were comprehensively investigated.

The use of extracellular DNA as a proxy for specific microbial activity.

The ubiquity and relevance of extracellular DNA (exDNA) are well-known and increasingly gaining importance in many fields of application such as medicine and environmental microbiology. Although sources and types of exDNA are manifold, ratios of specific DNA-molecules inside and outside of living cells can give reliable information about the activity of entire systems and of specific microbial groups or species. Here, we introduce a method to discriminate between internal (iDNA), as well as bound and free exDNA, and evaluate various DNA fractions and related ratios (ex:iDNA) regarding their applicability to be used as a fast, convenient, and reliable alternative to more tedious RNA-based activity measurements.

Anaerobic Fungi and Their Potential for Biogas Production.

Plant biomass is the largest reservoir of environmentally friendly renewable energy on earth. However, the complex and recalcitrant structure of these lignocellulose-rich substrates is a severe limitation for biogas production. Microbial pro-ventricular anaerobic digestion of ruminants can serve as a model for improvement of converting lignocellulosic biomass into energy.

Comparative evaluation of multiple methods to quantify and characterise granular anammox biomass.

Six methodologically different approaches were evaluated and compared regarding their suitability to quantify and characterise granular anammox biomass. The investigated techniques were gravimetric analysis (GA), activity measurements (AM), Coulter counter analysis (CC), quantitative PCR (qPCR), heme protein quantification (HQ) and the novel image analysis technique Particle Tracking (PT). The focus was set on the development of fast, economic and user-friendly approaches for potential implementation in regular wastewater treatment plant (WWTP) monitoring.

A novel fixed fibre biofilm membrane process for on-site greywater reclamation requiring no fouling control.

On-site greywater treatment and reuse in urban areas bears the potential to reduce huge quantities of wastewater and lower freshwater shortages. Until now dissemination of small, single household applications has been rather limited as simple and high quality water producing, but also cost-effective treatment units have not been developed so far. This paper proposes a new process, based on a concurrently working hollow-fibre membrane as fixed biofilm support and filtration device.

Finding a robust strain for biomethanation: anaerobic fungi (Neocallimastigomycota) from the Alpine ibex (Capra ibex) and their associated methanogens.

Anaerobic fungi occupy the rumen and digestive tract of herbivores, where they play an important role in enzymatic digestion of lignocellulosic and cellulosic substrates, i.e. organic material that their hosts are unable to decompose on their own.