Phylogenetic diversity and in situ detection of eukaryotes in anaerobic sludge digesters

Abstract

Eukaryotic communities in aerobic wastewater treatment processes are well characterized, but little is known about them in anaerobic processes. In this study, abundance, diversity and morphology of eukaryotes in anaerobic sludge digesters were investigated by quantitative real-time PCR (qPCR), 18S rRNA gene clone library construction and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Samples were taken from four different anaerobic sludge digesters in Japan. Results of qPCR of rRNA genes revealed that Eukarya accounted from 0.1% to 1.4% of the total number of microbial rRNA gene copy numbers. The phylogenetic affiliations of a total of 251 clones were Fungi, Alveolata, Viridiplantae, Amoebozoa, Rhizaria, Stramenopiles and Metazoa. Eighty-five percent of the clones showed less than 97.0% sequence identity to described eukaryotes, indicating most of the eukaryotes in anaerobic sludge digesters are largely unknown. Clones belonging to the uncultured lineage LKM11 in Cryptomycota of Fungi were most abundant in anaerobic sludge, which accounted for 50% of the total clones. The most dominant OTU in each library belonged to either the LKM11 lineage or the uncultured lineage A31 in Alveolata. Principal coordinate analysis indicated that the eukaryotic and prokaryotic community structures were related. The detection of anaerobic eukaryotes, including the members of the LKM11 and A31 lineages in anaerobic sludge digesters, by CARD-FISH revealed their sizes in the range of 2–8 μm. The diverse and uncultured eukaryotes in the LKM11 and the A31 lineages are common and ecologically relevant members in anaerobic sludge digester.

Biogas production and microbial community structure in a stable‐stage of a two‐stage anaerobic digester

“…Generally considered and regardless of the bioreactor, Rotifera and Phragmoplastophyta were the most representative phyla. In contrast to Matsubayashi et al, we found that Rotifera phylum is also abundant in anaerobic activated samples. Eukaryal phylotypes were mainly clustered to Fungi (42.2%), Animalia (28.8%), Protista (13.3%), and finally Plantae (8.9%).…”

“…A total of 38 different eukaryal OTUs were detected in the samples of the biomass from MC, AD, and MD (Figure S1C and Figure c). The role of eukaryotes during aerobic treatment processes have been associated with an excess of sludge production and performance and predation of bacteria but few studies have investigated the diversity of eukaryotes in anaerobic digestion . Generally considered and regardless of the bioreactor, Rotifera and Phragmoplastophyta were the most representative phyla.…”

Ten reasons why a sequence-based nomenclature is not useful for fungi anytime soon

“…If it is possible to publish new species from the computer just on the basis of a DNA sequence, not only knowledge of the morphology, anatomy, chemistry, physiology, life history strategies and ecology of fungi would lose value, but researchers interested in organismal mycology might be discouraged to intensely study and characterise species right from the start, eroding the foundation on which fungal systematics is built. If all the ‘dark matter’ of the cryptic basal lineages of fungi ( Grossart et al 2016 ) would be formally named based on sequence data, this would probably also discourage the laborious search for these organisms by FISH and other microscopy techniques ( Jones et al 2011 , Lazarus & James 2015 , Lepère et al 2016 , Matsubayashi et al 2017 ). Another problematic issue is that if sequence data were accepted as type, specimens might be seen as obsolete and only cost-prohibitive museum objects, as they are more difficult to store, curate and preserve than sequence data.…”

Process Disturbances in Agricultural Biogas Production—Causes, Mechanisms and Effects on the Biogas Microbiome: A Review

“…The biogas microbiome does not only comprise bacteria and archaea but also viruses/phages [7] as well as eukaryotes including fungi and protists (mainly protozoa) which are less investigated [8][9][10]. While it is assumed that the functional characteristics of pro-and eukaryotes are closely related to each other in a cooperative way [11], viruses/phages are suspected to have regulatory effects on the microbial cell turnover [7,12].…”