Domain Archaea Research Articles

Nitrate reduced arsenic redox transformation and transfer in flooded paddy soil-rice system

Inhibition of reductive transformation of arsenic (As) in flooded paddy soils is of fundamental importance for mitigating As transfer into food chain. Anaerobic arsenite (As(III)) oxidizers maintain As in less mobile fraction under nitrate-reducing conditions. In this study, we explored the dynamic profile of As speciation in porewater and As distribution among the pools of differential bioavailability in soil solid phase with and without nitrate treatment. In parallel, the abundance and diversity of As(III) oxidase gene (aioA) in flooded paddy soil with nitrate amendment was examined by quantitative PCR and aioA gene clone library. Furthermore, the impact of nitrate on As accumulation and speciation in rice seedlings was unraveled. With nitrate addition (25 mmol NO3− kg−1 soil), porewater As(III) was maintained at a consistently negligible concentration in the flooded paddy soil and the reductive dissolution of As-bearing Fe oxides/hydroxides was significantly restrained. Specifically, nitrate amendment kept 81% of total soil As in the nonlabile fraction with arsenate (As(V)) dominating after 30 days of flooding, compared to only 61% in the unamended control. Nitrate treatment induced 4-fold higher abundance of aioA gene, which belonged to domains of bacteria and archaea under the classes α-Proteobacteria (6%), ß-Proteobacteria (90%), ɣ-Proteobacteria (2%), and Thermoprotei (2%). By nitrate addition, As accumulation in rice seedlings was decreased by 85% with simultaneously elevated As(V) ratio in rice plant relative to control after 22 days of growth under flooded conditions. These results highlight that nitrate application can serve an efficient method to inhibit reductive dissolution of As in flooded paddy soils, and hence diminish As uptake by rice under anaerobic growing conditions.

FISH analysis of microbial communities in a full-scale technology for biogas production.

The anaerobic digestion is a biological process that consists of four stages. At the final step of the biodegradation of the organics the most sensitive to the ambient factors group of microorganisms - the methanogens, produces biogas with main component methane. Common problems of these technologies are low biogas yield, production of biogas with low quality or situations in which the plant gets out of exploitation. These problems are related to the lack of biological indicators of the process used in the practice and lack of understanding of the structure and functioning of the methanogenic consortium. Different fluorescent techniques have the potential to fulfill this gap and to contribute to the deep understanding of the structure of the microbial communities. In this study it was applied fluorescence in situ hybridization analysis for identifying and localization of microorganisms by the Archaea domain in digesters of wastewater treatment plant "Kubratovo". High negative correlation between the quantity of Archaea and the biogas and methane production has been registered. This method has the potential to be used as a tool for analyzing the structure of the microbial communities in the digesters and thus to allow the adaptation of the consortium and the optimization of the whole process.

The diversity of hydrogen-producing bacteria and methanogens within an in situ coal seam

BackgroundBiogenic and biogenic-thermogenic coalbed methane (CBM) are important energy reserves for unconventional natural gas. Thus, to investigate biogenic gas formation mechanisms, a series of fresh coal samples from several representative areas of China were analyzed to detect hydrogen-producing bacteria and methanogens in an in situ coal seam. Complete microbial DNA sequences were extracted from enrichment cultures grown on coal using the Miseq high-throughput sequencing technique to study the diversity of microbial communities. The species present and differences between the dominant hydrogen-producing bacteria and methanogens in the coal seam are then considered based on environmental factors.ResultsSequences in the Archaea domain were classified into four phyla and included members from Euryarchaeota, Thaumarchaeota, Woesearchaeota, and Pacearchaeota. The Bacteria domain included members of the phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria, Verrucomicrobia, Planctomycetes, Chloroflexi, and Nitrospirae. The hydrogen-producing bacteria was dominated by the genera: Clostridium, Enterobacter, Klebsiella, Citrobacter, and Bacillus; the methanogens included the genera: Methanorix, Methanosarcina, Methanoculleus, Methanobrevibacter, Methanobacterium, Methanofollis, and Methanomassiliicoccus.ConclusionTraces of hydrogen-producing bacteria and methanogens were detected in both biogenic and non-biogenic CBM areas. The diversity and abundance of bacteria in the biogenic CBM areas are relatively higher than in the areas without biogenic CBM. The community structure and distribution characteristics depend on coal rank, trace metal elements, temperature, depth and groundwater dynamic conditions. Biogenic gas was mainly composed of hydrogen and methane, the difference and diversity were caused by microbe-specific fermentation of substrates; as well as by the environmental conditions. This discovery is a significant contribution to extreme microbiology, and thus lays the foundation for research on biogenic CBM.

Application of microbial fuel cell technology for wastewater treatment and electricity generation under Nordic countries climate conditions: Study of performance and microbial communities

Two microbial fuel cells were inoculated with activated sludge from Finland and operated under moderate (25 °C) and low (8 °C) temperatures. Operation under real urban wastewater showed similarities in chemical oxygen demand removal and voltage generated, although moderate temperature supported higher ammonium oxidation. Fungi disappeared in the microbial fuel cell operated at temperature of 25 °C. Archaea domain was dominated by methanogenic archaea at both temperature scenarios. Important differences were observed in bacterial communities between both temperatures, however generating similar voltage. The results supported that the implementation of microbial fuel cells in Nordic countries operating under real conditions could be successful, as well as suggested the flexibility of cold-adapted inoculum for starting-up microbial fuel cells, regardless of the operating temperature of the system, obtaining higher COD removal and voltage generation performances at low temperature than at moderate temperature.

Environmental controls on the abundance of methanotrophs and methanogens in peat bog lakes

The aim of the present study was to identify the factors that influence the composition of methanogens and methanotrophs in the background prokaryotic community in peat bog lakes. We hypothesized that the microbial composition is a function of the physicochemical conditions of the water and a function of depth-dependent oxygen (DO) concentrations. To address this aim, we collected water samples from subsurface and near-bottom layers, representing oxic and anoxic conditions in 4 peat bog lakes in NE Poland. The structure of methanogenic Archaea and methane-oxidizing bacteria (MOB) was determined with double labeled-fluorescence in situ hybridization (DOPE-FISH).The results showed significant differences in Procaryota communities between the oxic (subsurface) and suboxic/anoxic (near-bottom) layers in peat bog lakes (t-test, p < 0.05). The methanogens from the Archaea domain were observed in anoxic periods, while methanotrophs were present regardless of water depth and season. The abundance of methanogens was inversely correlated with DO and CO2. Methanotrophs adapted better to the changing habitat conditions. The nonmetrical multidimensional scaling (NMS) and partial least square regression (PLS-R) models showed that the methanotrophs in subsurface layers are positively associated with temperature, DOC, and TON while negatively associated with pH. The DO availability is not a prerequisite condition for the presence of methanothrophs. The most important factors for MOB at the bottom were CO2 and TON. Due to a significant role of methanotrophs in the control of the methane emission flux rates, there is a need for further research on factors responsible for methanotroph development in peat bog lakes.

Metabolic routes involved in the removal of linear alkylbenzene sulfonate (LAS) employing linear alcohol ethoxylated and ethanol as co-substrates in enlarged scale fluidized bed reactor

In this study, the microbial community characterization and metabolic pathway identification involved in the linear alkylbenzene sulfonated (LAS) degradation from commercial laundry wastewater in a fluidized bed reactor (FBR) on an increased scale were performed using the Illumina MiSeq platform. Ethanol and non-ionic surfactant (LAE, Genapol C-100) were used as co-substrates. The FBR was operated in five operational phases: (I) synthetic substrate for inoculation; (II) 7.9 ± 4.7 mg/L LAS and 11.7 ± 6.9 mg/L LAE; (III) 19.4 ± 12.9 mg/L LAS, 19.6 ± 9.2 mg/L LAE and 205 mg/L ethanol; (IV) 25.9 ± 11 mg/L LAS, 19.5 ± 9.1 mg/L LAE and 205 mg/L ethanol and (V) 43.9 ± 18 mg/L LAS, 25 ± 9.8 mg/L LAE and 205 mg/L ethanol. At all operation phases, organic matter was removed from 40.4 to 85.1% and LAS removal was from 24.7 to 56%. Sulfate-reducing bacteria (SRB) were identified in the biofilm of FBR in all operational phases. Although the LAS promoted a toxic effect on the microbiota, this effect can be reduced when using biodegradable co-substrates, such as ethanol and LAE, which was observed in Phase IV. In this phase, there was a greater microbial diversity (Shannon index) and higher microorganism richness (Chao 1 index), both for the Domain Bacteria, and for the Domain Archaea.

Toward a mechanistic and physiological understanding of a ferredoxin:disulfide reductase from the domains Archaea and Bacteria

Disulfide reductases reduce other proteins and are critically important for cellular redox signaling and homeostasis. Methanosarcina acetivorans is a methane-producing microbe from the domain Archaea that produces a ferredoxin:disulfide reductase (FDR) for which the crystal structure has been reported, yet its biochemical mechanism and physiological substrates are unknown. FDR and the extensively characterized plant-type ferredoxin:thioredoxin reductase (FTR) belong to a distinct class of disulfide reductases that contain a unique active-site [4Fe-4S] cluster. The results reported here support a mechanism for FDR similar to that reported for FTR with notable exceptions. Unlike FTR, FDR contains a rubredoxin [1Fe-0S] center postulated to mediate electron transfer from ferredoxin to the active-site [4Fe-4S] cluster. UV-visible, EPR, and Mössbauer spectroscopic data indicated that two-electron reduction of the active-site disulfide in FDR involves a one-electron-reduced [4Fe-4S]1+ intermediate previously hypothesized for FTR. Our results support a role for an active-site tyrosine in FDR that occupies the equivalent position of an essential histidine in the active site of FTR. Of note, one of seven Trxs encoded in the genome (Trx5) and methanoredoxin, a glutaredoxin-like enzyme from M. acetivorans, were reduced by FDR, advancing the physiological understanding of FDR's role in the redox metabolism of methanoarchaea. Finally, bioinformatics analyses show that FDR homologs are widespread in diverse microbes from the domain Bacteria.

99mTc radiolabeled archaeosomes as a potential melanoma imaging agent

Background: Melanoma incidence is growing worldwide. Although recent advances in imaging, there isn`t still available a specific melanoma agent that can be used for melanoma staging. Archaeosomes may be defined as liposomes composed of one or more polar lipids extracted from the Archaea domain (Archaebacterium). Objective:  As liposomes have been used as vehicles for drugs and isotopes, the aim of this work was to 99mTc radiolabel archaeosomes and evaluates its potential role as a melanoma imaging agent.Methods: Archaeosomes were prepared by hand shaken method and were radiolabeled with 99mTc; Radiolabelling efficiency and purity was evaluated through different chromatographic systems. In vitro stability of 99mTc-DTPA-archaeosomes was performed through L-cysteine challenge.Results: Archaeosomes size distribution was determined by laser light scattering, having nanometer size between 90 and 120 nm. Radiolabelling efficiency was greater than 90%; 99mTc-DTPA-Archaeosomes presented a radiochemical purity superior to 80% evaluated 24 hours post radiolabelling. For the highest concentration of L-cysteine (30mM) and 1h incubation, radiochemical purity was 92.90 %, 6.41 % was bound to cysteine and 0.69 % remained as 99mTcO4- . Biodistribution and scintigraphic imaging studies in healthy C57 black mice showed high liver, spleen uptake and renal elimination. Melanoma bearing mice, had similar biodistribution as healthy mice but increased melanoma uptake, with T/M ratio of 46 ±3.7.Conclusions:  Our results show the feasibility of 99mTc radiolabelling archaeosomes and their potential role as a melanoma imaging agent.

Active and total microbial community dynamics and the role of functional genes bamA and mcrA during anaerobic digestion of phenol and p-cresol

The aim of the present work was to investigate the dynamics of microbial community at DNA and RNA level and the role of bamA and mcrA gene during anaerobic digestion of phenol and p-cresol. Anaerobic digestion was conducted in batch reactors and microbial community dynamics was analysed. Results showed that active microbial community was quite dissimilar in comparison to the total microbial community. Syntrophorhabdus and Bacillus were the dominant active bacterial genera whereas Methanosaeta together with Methanobacterium showed the highest potential activity in the Archaea domain indicating a relevant role of these microorganisms in the anaerobic process. Ecological Networks revealed dissimilar interactions at DNA and RNA level, being the latter a better descriptor of the known roles of dominant OTUs. QRT-PCR results showed that expression of bamA gene correlated positively with instantaneous degradation rate proving for first time its functionality and its relationship with the kinetics of the process.

Comparative analyses of whole-genome protein sequences from multiple organisms

Phylogenies based on entire genomes are a powerful tool for reconstructing the Tree of Life. Several methods have been proposed, most of which employ an alignment-free strategy. Average sequence similarity methods are different than most other whole-genome methods, because they are based on local alignments. However, previous average similarity methods fail to reconstruct a correct phylogeny when compared against other whole-genome trees. In this study, we developed a novel average sequence similarity method. Our method correctly reconstructs the phylogenetic tree of in silico evolved E. coli proteomes. We applied the method to reconstruct a whole-proteome phylogeny of 1,087 species from all three domains of life, Bacteria, Archaea, and Eucarya. Our tree was automatically reconstructed without any human decisions, such as the selection of organisms. The tree exhibits a concentric circle-like structure, indicating that all the organisms have similar total branch lengths from their common ancestor. Branching patterns of the members of each phylum of Bacteria and Archaea are largely consistent with previous reports. The topologies are largely consistent with those reconstructed by other methods. These results strongly suggest that this approach has sufficient taxonomic resolution and reliability to infer phylogeny, from phylum to strain, of a wide range of organisms.

Assessing Methanogenic Archaeal Community in Full Scale Anaerobic Sludge Digester Systems in Dubai, United Arab Emirates.

Introduction:Anaerobic digestion for methane production comprises of an exceptionally diverse microbial consortium, a profound understanding about which is still constrained. In this study, the methanogenic archaeal communities in three full-scale anaerobic digesters of a Municipal Wastewater Treatment Plant were analyzed by Fluorescence in situ hybridization and quantitative real-time Polymerase Chain Reaction (qPCR) technique.Methods & Materials:Fluorescence in situ hybridization (FISH) was performed to detect and quantify the methanogenic Archaea in the sludge samples whereas qPCR was carried out to support the FISH analysis. Multiple probes targeting domain archaea, different orders and families of Archaea were used for the studies.Results and Discussion:In general, the aceticlastic organisms (Methanosarcinaceae & Methanosaetaceae) were more abundant than the hydrogenotrophic organisms (Methanobacteriales, Methanomicrobiales, Methanobacteriaceae & Methanococcales). Both FISH and qPCR indicated that family Methanosaetaceae was the most abundant suggesting that aceticlastic methanogenesis is probably the dominant methane production pathway in these digesters.Conclusion:Future work involving high-throughput sequencing methods and correlating archaeal communities with the main operational parameters of anaerobic digesters will help to obtain a better understanding of the dynamics of the methanogenic archaeal community in wastewater treatment plants in United Arab Emirates (UAE) which in turn would lead to improved performance of anaerobic sludge digesters.

Use of Nitrates and Sulphates as Hydrogen Sink in Reducing Enteric Methane Production

Abstract Methane (CH4) and other gases like carbon dioxide (CO2), nitrous oxide (N2O), are green house gases (GHGs) that aggravates the effects of solar and thermal radiation on surface and atmospheric temperature. CH4 is the second largest GHG having 21 times more heat generation potential than CO2. Global livestock agriculture was responsible for 18% of the anthropogenic GHG emissions annually. CH4 production in the rumen accounts for 2–12 % loss of gross energy and consequently influence performance of ruminants. So, reducing ruminant CH4 emissions is an important objective for ensuring the sustainability of ruminant-based livestock farming. CH4 is formed in the rumen by methanogens (part of the domain Archaea), mainly from H2 and CO2. Within the rumen microbial food web, methanogens perform the beneficial task of removing H2, that allows reduced cofactors to be reoxidized and recycled, thereby enhancing the breakdown and fermentation of plant material. Therefore, rumen CH4 mitigation strategies need to consider alternative routes of H2 utilization. Nitrates and sulphates are potent inhibitors of CH4 in many anaerobic system including rumen; these salts have greater affinity for H2 as compared to CO2 resulting in net reduction in CH4 production. Experimental evidence suggest that nitrate and sulphate inhibit CH4 production both in vitro and in vivo without any adverse effect on rumen fermentation but the drawback is that nitrate is toxic to the animals; so supplementation at lower level helps the animal to acclimatize and reduces the chances of toxicity Keywords: Methane (CH4), sulphates, hydrogen, methanogens, fermentation Cite this Article Uniyal S, Mishra AK, Aswin K, et al. Use of Nitrates and Sulphates as Hydrogen Sink in Reducing Enteric Methane Production. Research & Reviews: Journal of Veterinary Science and Technology. 2016; 5(2): 5–8p.

RNases and Helicases in Gram-Positive Bacteria.

RNases are key enzymes involved in RNA maturation and degradation. Although they play a crucial role in all domains of life, bacteria, archaea, and eukaryotes have evolved with their own sets of RNases and proteins modulating their activities. In bacteria, these enzymes allow modulation of gene expression to adapt to rapidly changing environments. Today, >20 RNases have been identified in both Escherichia coli and Bacillus subtilis, the paradigms of the Gram-negative and Gram-positive bacteria, respectively. However, only a handful of these enzymes are common to these two organisms and some of them are essential to only one. Moreover, although sets of RNases can be very similar in closely related bacteria such as the Firmicutes Staphylococcus aureus and B. subtilis, the relative importance of individual enzymes in posttranscriptional regulation in these organisms varies. In this review, we detail the role of the main RNases involved in RNA maturation and degradation in Gram-positive bacteria, with an emphasis on the roles of RNase J1, RNase III, and RNase Y. We also discuss how other proteins such as helicases can modulate the RNA-degradation activities of these enzymes.

Methanogens in humans: potentially beneficial or harmful for health

Methanogens are anaerobic prokaryotes from the domain archaea that utilize hydrogen to reduce carbon dioxide, acetate, and a variety of methyl compounds into methane. Earlier believed to inhabit only the extreme environments, these organisms are now reported to be found in various environments including mesophilic habitats and the human body. The biological significance of methanogens for humans has been re-evaluated in the last few decades. Their contribution towards pathogenicity has received much less attention than their bacterial counterparts. In humans, methanogens have been studied in the gastrointestinal tract, mouth, and vagina, and considerable focus has shifted towards elucidating their possible role in the progression of disease conditions in humans. Methanoarchaea are also part of the human skin microbiome and proposed to play a role in ammonia turnover. Compared to hundreds of different bacterial species, the human body harbors only a handful of methanogen species represented by Methanobrevibacter smithii, Methanobrevibacter oralis, Methanosphaera stadtmanae, Methanomassiliicoccus luminyensis, Candidatus Methanomassiliicoccus intestinalis, and Candidatus Methanomethylophilus alvus. Their presence in the human gut suggests an indirect correlation with severe diseases of the colon. In this review, we examine the current knowledge about the methanoarchaea in the human body and possible beneficial or less favorable interactions.

Small RNAs of Haloferax mediterranei: Identification and Potential Involvement in Nitrogen Metabolism.

Small RNAs have been studied in detail in domains Bacteria and Eukarya but, in the case of the domain Archaea, the knowledge is scarce and the physiological function of these small RNAs (sRNAs) is still uncertain. To extend the knowledge of sRNAs in the domain Archaea and their possible role in the regulation of the nitrogen assimilation metabolism in haloarchaea, Haloferax mediterranei has been used as a model microorganism. The bioinformatic approach has allowed for the prediction of 295 putative sRNAs genes in the genome of H. mediterranei, 88 of which have been verified by means of RNA-Sequencing (RNA-Seq). The secondary structure of these sRNAs and their possible targets have been identified. Curiously, some of them present as possible target genes relating to nitrogen assimilation, such as glutamate dehydrogenase and the nitrogen regulatory PII protein. Analysis of RNA-Seq data has also revealed differences in the expression pattern of 16 sRNAs according to the nitrogen source. Consequently, RNomic and bioinformatic approaches used in this work have allowed for the identification of new sRNAs in H. mediterranei, some of which show different expression patterns depending on the nitrogen source. This suggests that these sRNAs could be involved in the regulation of nitrogen assimilation and can constitute an important gene regulatory network.

Presence of archaea and selected bacteria in infected root canal systems

Infections of the root canal have polymicrobial etiology. The main group of microflora in the infected pulp is bacteria. There is limited data that archaea may be present in infected pulp tissue. The aim of this study was to check the prevalence of archaea in necrotic root canal samples obtained from patients with primary or post-treatment infection. The prevalence of selected bacteria species (Prevotella intermedia, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Synergistes sp.) in necrotic samples was evaluated as well. Sixty-four samples from root canal were collected for DNA and RNA extraction. A PCR assay based on the 16S rRNA gene was used to determine the presence of archaea and selected bacteria. Of the 64 samples, 6 were analyzed by semiquantitative reverse transcription PCR to estimate expression profiles of 16S rRNA, and another 9 were selected for direct sequencing. Archaea were detected in 48.4% samples. Statistical analysis indicated a negative association in coexistence between archaea and Treponema denticola (P < 0.05; Pearson's χ2 test). The main representative of the Archaea domain found in infected pulp tissue was Methanobrevibacter oralis. Archaea 16S rRNA gene expression was significantly lower than Synergistes sp., Porphyromonas gingivalis, and Tannerella forsythia (P < 0.05; Student's t test). Thus, it can be hypothesized that archaea may participate in the endodontic microbial community.

Hydroxylamine released by nitrifying microorganisms is a precursor for HONO emission from drying soils

Nitrous acid (HONO) is an important precursor of the hydroxyl radical (OH), the atmosphere´s primary oxidant. An unknown strong daytime source of HONO is required to explain measurements in ambient air. Emissions from soils are one of the potential sources. Ammonia-oxidizing bacteria (AOB) have been identified as possible producers of these HONO soil emissions. However, the mechanisms for production and release of HONO in soils are not fully understood. In this study, we used a dynamic soil-chamber system to provide direct evidence that gaseous emissions from nitrifying pure cultures contain hydroxylamine (NH2OH), which is subsequently converted to HONO in a heterogeneous reaction with water vapor on glass bead surfaces. In addition to different AOB species, we found release of HONO also in ammonia-oxidizing archaea (AOA), suggesting that these globally abundant microbes may also contribute to the formation of atmospheric HONO and consequently OH. Since biogenic NH2OH is formed by diverse organisms, such as AOB, AOA, methane-oxidizing bacteria, heterotrophic nitrifiers, and fungi, we argue that HONO emission from soil is not restricted to the nitrifying bacteria, but is also promoted by nitrifying members of the domains Archaea and Eukarya.

The role of the surface smear microbiome in the development of defective smear on surface-ripened red-smear cheese

The complex smear microbiota colonizing the surface of red-smear cheese fundamentally impacts the ripening process, appearance and shelf life of cheese. To decipher the prokaryotic composition of the cheese smear microbiome, the surface of a semi-hard surface ripened cheese was studied post-ripening by culture-based and culture-independent molecular approaches. The aim was to detect potential bacterial alterations in the composition of the cheese smear microbiota resulting from cheese storage in vacuum film-prepackaging, which is often accompanied by the development of a surface smear defect. Next-generation sequencing of amplified 16S rRNA gene fragments revealed an unexpected high diversity of a total of 132 different genera from the domains Bacteria and Archaea on the cheese surface. Beside typical smear organisms, our study revealed the presence of several microorganisms so far not associated with cheese, but related to milk, farm and cheese dairy environments. A 16S ribosomal RNA based analysis from total RNA identified the major metabolically active populations in the cheese surface smear as Actinobacteria of the genera Corynebacterium, Brevibacterium, Brachybacterium and Agrococcus. Comparison of data on a higher phylogenetic level revealed distinct differences in the composition of the cheese smear microbiome from the different samples. While the proportions of Proteobacteria and Bacteroidetes were increased in the smear of prepacked samples and in particular in defective smear, staphylococci showed an opposite trend and turned out to be strongly decreased in defective smear. In conclusion, next-generation sequencing of amplified 16S rRNA genes and 16S rRNA from total RNA extracts provided a much deeper insight into the bacterial composition of the cheese smear microbiota. The observed shifts in the microbial composition of samples from defect surface smear suggest that certain members of the Proteobacteria contribute to the observed negative organoleptic properties of the surface smear of cheese after prepacking in plastic foil.

Host Specificity for Bacterial, Archaeal and Fungal Communities Determined for High- and Low-Microbial Abundance Sponge Species in Two Genera.

Sponges are engaged in intimate symbioses with a diversity of microorganisms from all three domains of life, namely Bacteria, Archaea and Eukarya. Sponges have been well studied and categorized for their bacterial communities, some displaying a high microbial abundance (HMA), while others show low microbial abundance (LMA). However, the associated Archaea and Eukarya have remained relatively understudied. We assessed the bacterial, archaeal and eukaryotic diversities in the LMA sponge species Dysidea avara and Dysidea etheria by deep amplicon sequencing, and compared the results to those in the HMA sponges Aplysina aerophoba and Aplysina cauliformis. D. avara and A. aerophoba are sympatric in the Mediterranean Sea, while D. etheria and A. cauliformis are sympatric in the Caribbean Sea. The bacterial communities followed a host-specific pattern, with host species identity explaining most of the variation among samples. We identified OTUs shared by the Aplysina species that support a more ancient association of these microbes, before the split of the two species studied here. These shared OTUs are suitable targets for future studies of the microbial traits that mediate interactions with their hosts. Even though the archaeal communities were not as rich as the bacterial ones, we found a remarkable diversification and specificity of OTUs of the family Cenarchaeaceae and the genus Nitrosopumilus in all four sponge species studied. Similarly, the differences in fungal communities were driven by sponge identity. The structures of the communities of small eukaryotes such as dinophytes and ciliophores (alveolates), and stramenopiles, could not be explained by either sponge host, sponge genus or geographic location. Our analyses suggest that the host specificity that was previously described for sponge bacterial communities also extends to the archaeal and fungal communities, but not to other microbial eukaryotes.

Anaerobic co-digestion of commercial laundry wastewater and domestic sewage in a pilot-scale EGSB reactor: The influence of surfactant concentration on microbial diversity

Different molecular tools (PCR-DGGE, 16S rRNA high-throughput sequencing and sequencing of the bamA gene) were used to assess and compare the microbial diversity in a pilot-scale expanded granular sludge bed (EGSB) reactor used for the anaerobic co-digestion of commercial laundry wastewater and domestic sewage and subjected to increasing concentrations of linear alkylbenzene sulfonate (LAS). Using PCR-DGGE, a microbial stratification along the sludge bed of the reactor was observed. When analyzed using 16S rRNA gene sequencing, the samples exhibited high microbial diversity and richness, with the lowest Shannon index obtained for the highest concentration of surfactant. For the Bacteria domain, the genera Bellilinea, Syntrophus, Syntrophobacter, Cytophaga, Bacteroides and Synergistes were the most abundant, whereas for the Archaea domain, the genera Methanosaeta and Methanolinea were predominant. The Pseudomonas genus was the only genus that was predicted to be involved in all steps of surfactant degradation. Additionally, bamA gene sequencing indicated the presence of the species Syntrophorhabdus aromaticivorans, Desulfosarcina cetonica and Syntrophus aciditrophicus, which have genetic potential for the aromatic ring cleavage under anaerobic conditions. Therefore, despite the high toxicity of LAS under anaerobic conditions, the use of different molecular tools revealed the great diversity and richness of the microbial community from the granular biomass of the EGSB pilot reactor, indicating that a microbial consortium is necessary for complete LAS degradation. Additionally, the sequencing analysis of the bamA gene represents a step forward in the understanding of the core microbial community involved in aromatic ring cleavage for anaerobic digestion of real laundry wastewater, which may guide future studies.