Nanohaloarchaea as beneficiaries of xylan degradation by haloarchaea

Climate change, desertification, salinisation of soils and the changing hydrology of the Earth are creating or modifying microbial habitats at all scales including the oceans, saline groundwaters and brine lakes. In environments that are saline or hypersaline, the biodegradation of recalcitrant plant and animal polysaccharides can be inhibited by salt-induced microbial stress and/or by limitation of the metabolic capabilities of halophilic microbes. We recently demonstrated that the chitinolytic haloarchaeon Halomicrobium can serve as the host for an ectosymbiont, nanohaloarchaeon 'Candidatus Nanohalobium constans'. Here, we consider whether nanohaloarchaea can benefit from the haloarchaea-mediated degradation of xylan, a major hemicellulose component of wood. Using samples of natural evaporitic brines and anthropogenic solar salterns, we describe genome-inferred trophic relations in two extremely halophilic xylan-degrading three-member consortia. We succeeded in genome assembly and closure for all members of both xylan-degrading cultures and elucidated the respective food chains within these consortia. We provide evidence that ectosymbiontic nanohaloarchaea is an active ecophysiological component of extremely halophilic xylan-degrading communities (although by proxy) in hypersaline environments. In each consortium, nanohaloarchaea occur as ectosymbionts of Haloferax, which in turn act as scavenger of oligosaccharides produced by xylan-hydrolysing Halorhabdus. We further obtained and characterised the nanohaloarchaea-host associations using microscopy, multi-omics and cultivation approaches. The current study also doubled culturable nanohaloarchaeal symbionts and demonstrated that these enigmatic nano-sized archaea can be readily isolated in binary co-cultures using an appropriate enrichment strategy. We discuss the implications of xylan degradation by halophiles in biotechnology and for the United Nation's Sustainable Development Goals.

Functional diversity of nanohaloarchaea within xylan-degrading consortia

Extremely halophilic representatives of the phylum Candidatus Nanohaloarchaeota (members of the DPANN superphyla) are obligately associated with extremely halophilic archaea of the phylum Halobacteriota (according to the GTDB taxonomy). Using culture-independent molecular techniques, their presence in various hypersaline ecosystems around the world has been confirmed over the past decade. However, the vast majority of nanohaloarchaea remain uncultivated, and thus their metabolic capabilities and ecophysiology are currently poorly understood. Using the (meta)genomic, transcriptomic, and DNA methylome platforms, the metabolism and functional prediction of the ecophysiology of two novel extremely halophilic symbiotic nanohaloarchaea (Ca. Nanohalococcus occultus and Ca. Nanohalovita haloferacivicina) stably cultivated in the laboratory as members of a xylose-degrading binary culture with a haloarchaeal host, Haloferax lucentense, was determined. Like all known DPANN superphylum nanoorganisms, these new sugar-fermenting nanohaloarchaea lack many fundamental biosynthetic repertoires, making them exclusively dependent on their respective host for survival. In addition, given the cultivability of the new nanohaloarchaea, we managed to discover many unique features in these new organisms that have never been observed in nano-sized archaea both within the phylum Ca. Nanohaloarchaeota and the entire superphylum DPANN. This includes the analysis of the expression of organism-specific non-coding regulatory (nc)RNAs (with an elucidation of their 2D-secondary structures) as well as profiling of DNA methylation. While some ncRNA molecules have been predicted with high confidence as RNAs of an archaeal signal recognition particle involved in delaying protein translation, others resemble the structure of ribosome-associated ncRNAs, although none belong to any known family. Moreover, the new nanohaloarchaea have very complex cellular defense mechanisms. In addition to the defense mechanism provided by the type II restriction-modification system, consisting of Dcm-like DNA methyltransferase and Mrr restriction endonuclease, Ca. Nanohalococcus encodes an active type I-D CRISPR/Cas system, containing 77 spacers divided into two loci. Despite their diminutive genomes and as part of their host interaction mechanism, the genomes of new nanohaloarchaea do encode giant surface proteins, and one of them (9,409 amino acids long) is the largest protein of any sequenced nanohaloarchaea and the largest protein ever discovered in cultivated archaea.

[Antagonistic activity of novel green microalgae strain]

AIM

Screening of novel microalgae strains for the presence of pronounced antagonistic (antibacterial) activity against opportunistic bacteria.

MATERIALS AND METHODS

11 pure cultures of green unicellular algae isolated from fresh and salt basins of Orenburg region were studied for the presence of antagonistic activity against 4 test-strains of opportunistic bacteria by a photometric method. The effect of water extracts of microalgae Astermonas gracilis on the speed of self-purification of brine from Escherichia coli as well as antibacterial activity of peloid were evaluated under co-cultivation conditions.

RESULTS

Pure cultures of green unicellular algae Scenedesmus obliquus (Turpin) Kütz, Scenedesmus magnus Meyen var. magnus, Pediastru duplex Meyen var. duplex, Chlorella vulgaris Bory, Monoraphidium arcuatum (Korschikov) Hindak (=Ankistrodesmus arcuatus Korschikov), Dictyosphaerium sp. had the most pronounced antagonistic activit against opportunistic bacteria. Water extract ofA. gracilis microalgae accelerated brine self-purification fro E. coli due to antibacterial effect. Peloid containing extracts of microorganism cells had a pronounced antibacterial effect against opportunistic bacteria.

CONCLUSION

Antagonistic substances localized inside cells of microalgae increased the speed of allochthonic microorganism elimination that is one of the mechanisms of self-purification of a basin and antibacterial effect of peloid. The novel green microalgae strains studied due to the presence of pronounced antagonistic activity may have a wide practical application.

[Experimental interaction of halophilic prokaryotes and opportunistic bacteria in brine]

AIM

Study the effect of extremely halophilic archaea and moderately halophilic bacteria on preservation of opportunistic bacteria in brine.

MATERIALS AND METHODS

17 strains of moderately halophilic bacteria and 2 strains of extremely halophilic archaea were isolated from continental hypersaline lake Razval of Sol-Iletsk area of Orenburg Region. Identification of pure cultures of prokaryotes was carried out taking into account their phenotype properties and based on determination of 16S RNA gene sequence. The effect of halophilic prokaryote on elimination of Escherichia coli from brine was evaluated during co-cultivation. Antagonistic activity of cell extracts of the studied microorganisms was evaluated by photometric method.

RESULTS

A more prolonged preservation of an E. coli strain in brine in the presence of live cells of extremely halophilic archaea Halorubrum tebenquichense and moderately halophilic bacteria Marinococcus halophilus was established. Extracts of cells of extremely halophilic archaea and moderately halophilic bacteria on the contrary displayed antagonistic activity.

CONCLUSION

The protective effect of live cells of halophilic prokaryotes and antagonistic activity of their cell extracts change the period of conservation of opportunistic bacteria in brine that regulates inter-microbial interactions and changes the period of self-purification that reflects the sanitary condition of a hypersaline water body.

[Persistent properties of microorganisms inhabiting highly mineralized water bodies]

AIM

Study prevalence and intensity of persistent properties in bacteria inhabiting highly min eralized water bodies and determine their role in interaction with halophilous heterotrophic protozoa.

MATERIALS AND METHODS

300 bacteria strains and 3 cultures of heterotrophic protozo isolated from water bodies with mineralization of 2-350 g/l were studied. Antilysozyme (ALA) antihistone (AHA) activity of bacteria, protozoa lysozyme were evaluated by dish and photometric methods. Protozoa histones were evaluated cytochemically. Interaction of protozoa and Escherichia coli was evaluated by experimental co-cultivation.

RESULTS

Presence of lysozyme an histones was shown in halophilous heterotrophic protozoa. Prevalence of ALA and AHA in bacteria was shown to increase as water body mineralization decreases. Intensity of E. colielimination from brine was determined to depend on the bacteria ALA level and phagocytic activity of protozoa. Participation of halotolerant protozoa in formation of heterogeneity of bacterial population by ALA was shown.

CONCLUSION

In biocenoses of highly mineralized water bodies functioning of lysozyme-antilysozyme, histone-antihistone systems was shown. Bacteria with high persistent potential may impair sanitary parameters of highly mineralized water bodies, process of self-purification of which depends directly on phagocytic activity of protozoa.

[Regulation of symbiotic interactions in algobacterial associations]

AIM

To study mechanisms of survival and regulation of natural algobacterial associations.

MATERIALS AND METHODS

Lysozyme, antilysozyme, catalase and antagonistic activity as well as hydrogen peroxide production were determined in algobacterial associations formed by green algae or cyanobacteria and satellite bacteria. For assessment of reactions of microbial interactions, derivates of Escherichia coli, which differ on the presence of antilysozyme and catalase signs, were used.

RESULTS

Multidirectional effects of symbionts in biocenosis were revealed. Involvement of functional systems lysozyme-antilysozyme and hydrogen peroxide-catalase in regulation of associative interactions in algae-bacterial biocenosis was established. In conditions of antibacterial action of algae's hydrogen peroxide, catalase activity of associate bacteria provides survival of microorganisms in association with algae, whereas high level of catalase activity promotes domination of associate bacteria in algobacterial communities. Antagonistic activity allows the microalgae to suppress growth of undesirable microorganisms and regulate their number in algobacterial cenosis.

CONCLUSION

Functional systems lysozyme-antilysozyme, hydrogen peroxide-catalase as well as antagonistic activity of symbionts form the basis for regulation of symbiotic interactions in associations of water microorganisms, which has ecological and sanitary-hygienic implications.

[Symbiosis in survival of microorganisms in hyperhaline water reservours]

Differently directed effects from autochthonous algae and bacteria on allochthonous microflora in hyperosmotic conditions were revealed and analyzed. Living halophilic microorganisms increase survival time of enterobacteria. Cellular extracts from halophils decrease storage time of allochthonous bacteria in a highly mineralized medium. Allochthonous bacteria in hyperosmotic conditions are able to suppress viability of autochthonous halophilic microflora. Symbiotic interactions between autochthonous and allochthonous microorganisms, defined by correlation of protective and antagonistic effects, regulate survival of microorganisms in hyperhaline water reservours and can be used for the assessment of their ecological and sanitary-and-hygienic states.

[Propagation of congenital anomalies of sexual development in the newborn population of Moscow]

The prevalence of congenital abnormalities of the genitals was estimated in newborns of the Moscow population in 1992 and 1993. The prevalence was found to be one case per 1500-1550 newborns. The pattern and structure of the observed pathology were studied. The range of patients who were not detected during the study, due to clinical peculiarities of their pathology, was estimated.