Environmental Microbiology

Summary The anaerobic oxidation of methane (AOM) is mediated by consortia of anaerobic methane‐oxidizing archaea (ANME) and their specific partner bacteria. In thermophilic AOM consortia enriched from Guaymas Basin, members of the ANME‐1 clade are associated with bacteria of the HotSeep‐1 cluster, which likely perform direct electron exchange via nanowires. The partner bacterium was enriched with hydrogen as sole electron donor and sulfate as electron acceptor. Based on phylogenetic, genomic and metabolic characteristics we propose to name this chemolithoautotrophic sulfate reducer Candidatus Desulfofervidus auxilii. Ca . D. auxilii grows on hydrogen at temperatures between 50°C and 70°C with an activity optimum at 60°C and doubling time of 4–6 days. Its genome draft encodes for canonical sulfate reduction, periplasmic and soluble hydrogenases and autotrophic carbon fixation via the reductive tricarboxylic acid cycle. The presence of genes for pili formation and cytochromes, and their similarity to genes of Geobacter spp., indicate a potential for syntrophic growth via direct interspecies electron transfer when the organism grows in consortia with ANME. This first ANME‐free enrichment of an AOM partner bacterium and its characterization opens the perspective for a deeper understanding of syntrophy in anaerobic methane oxidation.

Summary The bacterial tree contains many deep‐rooting clades without any cultured representatives. One such clade is ‘ E ndomicrobia’, a class‐level lineage in the phylum E lusimicrobia represented so far only by intracellular symbionts of termite gut flagellates. Here, we report the isolation and characterization of the first free‐living member of this clade from sterile‐filtered gut homogenate of defaunated (starch‐fed) R eticulitermes santonensis . Strain R sa215 is a strictly anaerobic ultramicrobacterium that grows exclusively on glucose, which is fermented to lactate, acetate, hydrogen and CO 2 . Ultrastructural analysis revealed a G ram‐negative cell envelope and a peculiar cell cycle. The genome contains a single set of nif genes that encode homologues of G roup IV nitrogenases, which were so far considered to have functions other than nitrogen fixation. We documented nitrogenase activity and diazotrophic growth by measuring acetylene reduction activity and 15 N 2 incorporation into cell mass, and demonstrated that transcription of nifH and nitrogenase activity occur only in the absence of ammonium. Based on the ancestral relationship to ‘ C andidatus   E ndomicrobium trichonymphae’ and other obligate endosymbionts, we propose the name ‘ E ndomicrobium proavitum ’ gen. nov., sp. nov. for the first isolate of this lineage and the name ‘ E ndomicrobia ’ class. nov. for the entire clade.

Summary Gold ore processing uses cyanide ( CN − ), which often results in large volumes of thiocyanate‐ ( SCN − ) contaminated wastewater requiring treatment. Microbial communities can degrade SCN − and CN − , but little is known about their membership and metabolic potential. Microbial‐based remediation strategies will benefit from an ecological understanding of organisms involved in the breakdown of SCN − and CN − into sulfur, carbon and nitrogen compounds. We performed metagenomic analysis of samples from two laboratory‐scale bioreactors used to study SCN − and CN − degradation. Community analysis revealed the dominance of Thiobacillus spp., whose genomes harbour a previously unreported operon for SCN − degradation. Genome‐based metabolic predictions suggest that a large portion of each bioreactor community is autotrophic, relying not on molasses in reactor feed but using energy gained from oxidation of sulfur compounds produced during SCN − degradation. Heterotrophs, including a bacterium from a previously uncharacterized phylum, compose a smaller portion of the reactor community. Predation by phage and eukaryotes is predicted to affect community dynamics. Genes for ammonium oxidation and denitrification were detected, indicating the potential for nitrogen removal, as required for complete remediation of wastewater. These findings suggest optimization strategies for reactor design, such as improved aerobic/anaerobic partitioning and elimination of organic carbon from reactor feed.

Summary To date, six candidate genera of anaerobic ammonium‐oxidizing (anammox) bacteria have been identified, and numerous studies have been conducted to understand their ecophysiology. In this study, we examined the physiological characteristics of an anammox bacterium in the genus ‘ C andidatus   J ettenia’. Planctomycete KSU ‐1 was found to be a mesophilic (20–42.5°C) and neutrophilic ( pH 6.5–8.5) bacterium with a maximum growth rate of 0.0020 h −1 . Planctomycete KSU ‐1 cells showed typical physiological and structural features of anammox bacteria; i.e. 29 N 2 gas production by coupling of 15 NH 4 + and 14 NO 2 − , accumulation of hydrazine with the consumption of hydroxylamine and the presence of anammoxosome. In addition, the cells were capable of respiratory ammonification with oxidation of acetate. Notably, the cells contained menaquinone‐7 as a dominant respiratory quinone. Proteomic analysis was performed to examine underlying core metabolisms, and high expressions of hydrazine synthase, hydrazine dehydrogenase, hydroxylamine dehydrogenase, nitrite/nitrate oxidoreductase and carbon monoxide dehydrogenase/acetyl‐ CoA synthase were detected. These proteins require iron or copper as a metal cofactor, and both were dominant in planctomycete KSU ‐1 cells. On the basis of these experimental results, we proposed the name ‘ C a . J ettenia caeni’ sp. nov. for the bacterial clade of the planctomycete KSU ‐1.

Summary In an acetate‐fed anaerobic–aerobic membrane bioreactor with deteriorated enhanced biological phosphorus removal ( EBPR ), D efluviicoccus ‐related tetrad‐forming organisms ( DTFO ) were observed to predominate in the microbial community. Using metagenomics, a partial genome of the predominant DTFO , ‘ C andidatus   D efluviicoccus tetraformis strain TFO 71’, was successfully constructed and characterized. Examining the genome confirmed the presence of genes related to the synthesis and degradation of glycogen and polyhydroxyalkanoate ( PHA ), which function as energy and carbon storage compounds. TFO 71 and ‘ C andidatus   A ccumulibacter phosphatis’ ( CAP ) UW ‐1 and CAP UW ‐2, representative polyphosphate‐accumulating organisms ( PAO ), have PHA metabolism‐related genes with high homology, but TFO 71 has unique genes for PHA synthesis, gene regulation and granule management. We further discovered genes encoding DTFO polyphosphate ( polyP ) synthesis, suggesting that TFO 71 may synthesize polyP under untested conditions. However, TFO 71 may not activate these genes under EBPR conditions because the retrieved genome does not contain all inorganic phosphate transporters that are characteristic of PAOs ( CAP UW ‐1, CAP UW ‐2, M icrolunatus phosphovorus   NM ‐1 and T etrasphaera species). As a first step in characterizing EBPR ‐associated DTFO metabolism, this study identifies important differences between DTFO and PAO that may contribute to EBPR community competition and deterioration.

Summary Many hemipterans are associated with symbiotic bacteria, which are usually found intracellularly in specific bacteriomes. In this study, we provide the first molecular identification of the bacteriome‐associated, obligate endosymbiont in a G ondwanan relict insect taxon, the moss bugs ( H emiptera: C oleorrhyncha: P eloridiidae), which represents one of the oldest lineages within the H emiptera. Endosymbiotic associations of fifteen species of the family were analysed, covering representatives from S outh A merica, A ustralia/ T asmania and N ew Z ealand. Phylogenetic analysis based on four kilobases of 16 S –23 S r RNA gene fragments showed that the obligate endosymbiont of P eloridiidae constitute a so far unknown group of G ammaproteobacteria which is named here ‘ Candidatus Evansia muelleri’. They are related to the sternorrhynchous endosymbionts C andidatus   P ortiera and C andidatus   C arsonella. Comparison of the primary‐endosymbiont and host ( COI  + 28 S rRNA ) trees showed overall congruence indicating co‐speciation the hosts and their symbionts. The distribution of the endosymbiont within the insect body and its transmission was studied using FISH . The endosymbionts were detected endocellularly in a pair of bacteriomes as well as in the ‘symbiont ball’ of the posterior pole of each developing oocyte. Furthermore, ultrastructural analysis of the M alpighian tubules revealed that most host nuclei are infected by an endosymbiotic, intranuclear bacterium that was determined as an A lphaproteobacterium of the genus R ickettsia .

Summary Knowledge of intraspecific variation in symbioses may aid in understanding the ecology of widespread insects in different parts of their range. We investigated bacterial symbionts of A delges tsugae , a pest of hemlocks in eastern N orth A merica introduced from A sia. Amplification, cloning, and sequencing of bacterial 16 S rDNA , in situ hybridizations, and electron microscopy revealed that A . tsugae harbours up to five bacterial phylotypes, according to population. Three G ammaproteobacteria species are maternally transmitted. The first, designated ‘ C a . P seudomonas adelgestsugas’ resides in the haemocoel, and was detected in all populations except T aiwan. The second phylotype, ‘ C a . S erratia symbiotica’, resides in bacteriocytes of populations on T suga sieboldii in J apan and in E . N orth A merica. The third phylotype, designated ‘ C a . A nnandia adelgestsuga’, clustered within a lineage of several insect endosymbionts that included B uchnera aphidicola . It was detected in bacteriocytes in all populations, and in salivary glands of first instars. Two B etaproteobacteria phylotypes were detected in some J apanese T . sieboldii and eastern N orth A merica populations, and were observed only in salivary glands with no evidence of maternal transmission. Our results support the ideas that symbiont gain and loss has been volatile in adelgids, and that symbionts may help to trace the source of invasive species.

Summary A novel moderately thermophilic, facultatively anaerobic chemoorganotrophic bacterium strain P3M ‐2 T was isolated from a microbial mat developing on the wooden surface of a chute under the flow of hot water (46° C ) coming out of a 2775‐m‐deep oil exploration well ( T omsk region, R ussia). Strain P3M ‐2 T is a moderate thermophile and facultative anaerobe growing on mono‐, di‐ or polysaccharides by aerobic respiration, fermentation or by reducing diverse electron acceptors [nitrite, F e( III ), As ( V )]. Its closest cultivated relative (90.8% rRNA gene sequence identity) is I gnavibacterium album , the only chemoorganotrophic member of the phylum C hlorobi . New genus and species M elioribacter roseus are proposed for isolate P3M ‐2 T . Together with I . album , the new organism represents the class I gnavibacteria assigned to the phylum Chlorobi . The revealed group includes a variety of uncultured environmental clones, the 16S rRNA gene sequences of some of which have been previously attributed to the candidate division ZB1 . Phylogenetic analysis of M . roseus and I . album based on their 23S rRNA and RecA sequences confirmed that these two organisms could represent an even deeper, phylum‐level lineage. Hence, we propose a new phylum Ignavibacteriae within the Bacteroidetes – C hlorobi group with a sole class I gnavibacteria , two families I gnavibacteriaceae and M elioribacteraceae and two species I . album and M . roseus . This proposal correlates with chemotaxonomic data and phenotypic differences of both organisms from other cultured representatives of C hlorobi . The most essential differences, supported by the analyses of complete genomes of both organisms, are motility, facultatively anaerobic and obligately organotrophic mode of life, the absence of chlorosomes and the apparent inability to grow phototrophically.

Summary Gill disease in salmonids is characterized by a multifactorial aetiology. Epitheliocystis of the gill lamellae caused by obligate intracellular bacteria of the order Chlamydiales is one known factor; however, their diversity has greatly complicated analyses to establish a causal relationship. In addition, tracing infections to a potential environmental source is currently impossible. In this study, we address these questions by investigating a wild brown trout ( Salmo trutta ) population from seven different sites within a Swiss river system. One age class of fish was followed over 18 months. Epitheliocystis occurred in a site‐specific pattern, associated with peak water temperatures during summer months. No evidence of a persistent infection was found within the brown trout population, implying an as yet unknown environmental source. For the first time, we detected ‘ Candidatus Piscichlamydia salmonis’ and ‘ Candidatus Clavochlamydia salmonicola’ infections in the same salmonid population, including dual infections within the same fish. These organisms are strongly implicated in gill disease of caged Atlantic salmon in Norway and Ireland. The absence of aquaculture production within this river system and the distance from the sea, suggests a freshwater origin for both these bacteria and offers new possibilities to explore their ecology free from aquaculture influences.

Summary The name Arthromitus has been applied collectively to conspicuous filamentous bacteria found in the hindguts of termites and other arthropods. First observed by Joseph Leidy in 1849, the identity of these filaments has remained contentious. While Margulis and colleagues declared them to be a life stage of Bacillus cereus , others have assumed them to belong to the same lineage as the segmented filamentous bacteria (SFB) from vertebrate guts, a group that has garnered much attention due to their unique ability to specifically modulate their host's immune response. Both SFB and Arthromitus filaments from arthropod guts were grouped under provisional name ‘ Candidatus Arthromitus’ by Snel and colleagues as they share a striking similarity in terms of their morphology and close contact to the host gut wall. While SFB form a distinct lineage within the family Clostridiaceae , the identity of the filaments from arthropod guts remains elusive. Using whole‐genome amplification of single filaments capillary picked from termite guts and fluorescence in situ hybridization of 16S rRNA with group‐specific oligonucleotide probes, we show that they represent a monophyletic lineage within the family Lachnospiraceae distinct from that of SFB. Therefore, ‘ Candidatus Arthromitus’ can no longer be used for both groups. Given the historic precedence, we propose to reserve this name for the filaments that were originally described by Leidy. For the SFB from vertebrate guts, we propose the provisional name ‘ Candidatus Savagella’ in honour of the American gut microbiologist Dwayne C. Savage, who was the first to describe that important bacterial group.