Haloarchaea as Promising Chassis to Green Chemistry

Climate change and the scarcity of primary resources are driving the development of new, more renewable and environmentally friendly industrial processes. As part of this green chemistry approach, extremozymes (extreme microbial enzymes) can be used to replace all or part of the chemical synthesis stages of traditional industrial processes. At present, the production of these enzymes is limited by the cellular chassis available. The production of a large number of extremozymes requires extremophilic cellular chassis, which are not available. This is particularly true of halophilic extremozymes. The aim of this review is to present the current potential and challenges associated with the development of a haloarchaea-based cellular chassis. By overcoming the major obstacle of the limited number of genetic tools, it will be possible to propose a robust cellular chassis for the production of functional halophilic enzymes that can participate in the industrial transition of many sectors.

Genome-based classification of the class Halobacteria and description of Haladaptataceae fam. nov. and Halorubellaceae fam. nov

Currently, there are four mainstream taxonomic opinions on the classification of the class Halobacteria at the family and order levels. The International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halobacteria (ICSP), List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Centre for Biotechnology Information (NCBI) adopted taxonomies have three to four orders and up to eight families, while the Genome Taxonomy Database (GTDB) taxonomy proposes only one order with nine families. To resolve the taxonomic inconsistency, phylogenomic analyses based on concatenated single-copy orthologous proteins and 122 concatenated conserved single-copy marker proteins were conducted to infer the taxonomic status of the current representatives of the class Halobacteria at the family and order levels. The current 76 genera with validly published names of the class Halobacteria were able to be assigned into eight families in one order. On the basis of these results, it is proposed that the current species with validly published names of the class Halobacteria should be remerged into the order Halobacteriales, then assigned to eight families, Haladaptataceae, Haloarculaceae, Halobacteriaceae, Halococcaceae, Haloferacaceae, Natronoarchaeaceae, Natrialbaceae and Halorubellaceae. Thus, Haladaptataceae fam. nov. is described based on Haladaptatus, Halomicrococcus and Halorussus and Halorubellaceae fam. nov. is proposed incorporating Haloarchaeobius and Halorubellus, respectively.

Cellular differentiation into hyphae and spores in halophilic archaea

Several groups of bacteria have complex life cycles involving cellular differentiation and multicellular structures. For example, actinobacteria of the genus Streptomyces form multicellular vegetative hyphae, aerial hyphae, and spores. However, similar life cycles have not yet been described for archaea. Here, we show that several haloarchaea of the family Halobacteriaceae display a life cycle resembling that of Streptomyces bacteria. Strain YIM 93972 (isolated from a salt marsh) undergoes cellular differentiation into mycelia and spores. Other closely related strains are also able to form mycelia, and comparative genomic analyses point to gene signatures (apparent gain or loss of certain genes) that are shared by members of this clade within the Halobacteriaceae. Genomic, transcriptomic and proteomic analyses of non-differentiating mutants suggest that a Cdc48-family ATPase might be involved in cellular differentiation in strain YIM 93972. Additionally, a gene encoding a putative oligopeptide transporter from YIM 93972 can restore the ability to form hyphae in a Streptomyces coelicolor mutant that carries a deletion in a homologous gene cluster (bldKA-bldKE), suggesting functional equivalence. We propose strain YIM 93972 as representative of a new species in a new genus within the family Halobacteriaceae, for which the name Actinoarchaeum halophilum gen. nov., sp. nov. is herewith proposed. Our demonstration of a complex life cycle in a group of haloarchaea adds a new dimension to our understanding of the biological diversity and environmental adaptation of archaea.

Halocatena marina sp. nov., a novel filamentous halophilic archaeon isolated from marine tidal flat and emended description of the genus Halocatena

Three novel filamentous halophilic archaea, strains DFN5^T, RDMS1, and QDMS1, were isolated from the coastal saline soil samples of the intertidal zones located in different regions of Jiangsu Province, China. The colonies of these strains were pinkish-white due to the presence of white spores. These three strains are extremely halophilic and grew optimally at 35-37 °C and pH 7.0-7.5. Based on 16S rRNA and rpoB' gene analysis, strains DFN5^T, RDMS1, and QDMS1 gathered together in phylogenetic trees and then clustered with the current species of the genus Halocatena showing 96.9-97.4% and 82.2-82.5% similarities, respectively. Both the 16S rRNA gene-based and rpoB' gene-based phylogenies were fully supported by the phylogenomic analysis, and the overall genome-related indexes indicated that strains DFN5^T, RDMS1, and QDMS1 should be a novel species of the genus Halocatena. Genome mining revealed that there are considerable differences in the genes related to β-carotene synthesis among these three strains and the current species of Halocatena. The major polar lipids of strains DFN5^T, RDMS1, and QDMS1 are PA, PG, PGP-Me, S-TGD-1, TGD-1, and TGD-2. The minor polar lipids, S-DGD-1, DGD-1, S₂-DGD, and S-TeGD may be detected. According to the phenotypic characteristics, phylogenetic analysis, genomic and chemotaxonomic features, strains DFN5^T (= CGMCC 1.19401 ^T = JCM 35422 ^T), RDMS1 (= CGMCC 1.19411) and QDMS1 (= CGMCC 1.19410) were classified as a novel species of the genus Halocatena with the proposed name, Halocatena marina sp. nov. This is the first report of the description of a novel filamentous haloarchaeon isolated from marine intertidal zones.

Halocatena salina sp. nov., a filamentous halophilic archaeon isolated from Aiding Salt Lake

A filamentous cell-shaped halophilic archaeon (strain AD-1^T) was isolated from Aiding Salt Lake, PR China. Its colonies on HCM7 agar plates were pinkish white, 1-4 mm (diameter), elevated and round. The optimum conditions for growth were observed at 42 °C, 4.3 M NaCl, 0.01 M MgCl₂ and pH 7. Strain AD-1^T could hydrolyse Tween 60, Tween 80, starch and gelatin. Phylogenetic analysis based on 16S rRNA gene, rpoB' and the concatenated 484 single-copy orthologous proteins revealed that strain AD-1^T formed a clade with Halocatena pleomorpha SPP-AMP-1^T. The average nucleotide identity and in silico DNA-DNA hybridization values between strain AD-1^T and Halocatena pleomorpha SPP-AMP-1^T were both below the species delineation thresholds (95~96 and 70 %, respectively). The major phospholipids of strain AD-1^T were phosphatidic acid, phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, while the major glycolipids were sulphated galactosyl mannosyl glucosyl diether, galactosyl mannosyl glucosyl diether and glucosyl mannosyl glucosyl diether. The phenotypic, phylogenetic and genome-based analyses suggested that strain AD-1^T (=CGMCC 1.13724^T=JCM 32960^T) represents a novel species, for which the name Halocatena salina sp. nov. is proposed.

Improving soil fertility by driving microbial community changes in saline soils of Yellow River Delta under petroleum pollution

It is promising to use indigenous microorganisms for fertility improvement in petroleum-contaminated coastal soil. As a result, the microbial community and physicochemical property are the base for the restoration. For the detailed information, the Phragmites Communis (P), Chinese Tamarisk (C), Suaeda salsa (S), and new Bare Land (B) soil of Yellow River Delta was 90 g in 100 mL sterile bottles simulated at 25 °C with soil: petroleum = 10:1 in the incubator for four months. The samples were detected at 60 and 120 days along with untreated soil and aged Oil Sludge (O) as control. The results showed that all the samples were alkaline (pH 7.99-8.83), which the salinity and NO₃^- content of incubate soil followed the in situ samples as P (1.09-1.72‰, 8.02-8.17 mg kg^-1), C (10.61-13.79‰, 5.99-6.07 mg kg^-1), S (10.19-12.43‰, 3.64-4.22 mg kg^-1), B (31.85-32.45‰, 3.56-3.72 mg kg^-1) and O (31.61-34.30‰, 0.89-0.90 mg kg^-1). NO₃^- and organic carbon decreased after incubation, which the polluted samples (86.63-92.63 g kg^-1) still had higher organic carbon than untreated ones with more NH₄⁺ consumption. The high-throughput sequence results showed that the Gammaproteobacteria and Alphaproteobacteria were dominant in all samples, while sulfate reducting bacteria Alphaproteobacteria decreased at 120 days. Meanwhile, the electroactive Gammaproteobacteria might symbiosis with Methanosaetaceae and Methanosarcinaceae, degrading petroleum after electron receptors depletion. Nitrososphaeraceae and Nitrosopumilaceae oxidise NH₄⁺ to NO₂^- for intra-aerobic anaerobes and denitrifying bacteria producing oxygen for biodegradation in polluted Phragmites Communis soil. The halotolerant Halomicrobiaceae and Haloferacaceae predominated in saline Chinese Tamarisk, Suaeda Salsa and Bare Land, which were potential electroactive degradater. As the ageing sludge formed, the hydrogen trophic methanogens Methanothermobacteraceae (73.90-92.72%) was prevalent with the petroleum pollution. In conclusion, petroleum initiated two-phase in the sludge forming progress: electron acceptor consumption and electron transfer between degradater and methanogens. Based on the results, the domestic sewage N, P removal coupling and electron transport will be the basement for polluted soils fertility improvement.

Cultivation of halophilic archaea (class Halobacteria) from thalassohaline and athalassohaline environments

As a group, the halophilic archaea (class Halobacteria) are the most salt-requiring and salt-resistant microorganisms within the domain Archaea. Halophilic archaea flourish in thalassohaline and athalassohaline environments and require over 100-150 g/L NaCl for growth and structural stability. Natural hypersaline environments vary in salt concentration, chemical composition and pH, and occur in climates ranging from tropical to polar and even under-sea. Accordingly, their resident haloarchaeal species vary enormously, as do their individual population compositions and community structures. These diverse halophilic archaeal strains are precious resources for theoretical and applied research but assessing their taxonomic and metabolic novelty and diversity in natural environments has been technically difficult up until recently. Environmental DNA-based high-throughput sequencing technology has now matured sufficiently to allow inexpensive recovery of massive amounts of sequence data, revealing the distribution and community composition of halophilic archaea in different hypersaline environments. While cultivation of haloarchaea is slow and tedious, and only recovers a fraction of the natural diversity, it is the conventional means of describing new species, and provides strains for detailed study. As of the end of May 2020, the class Halobacteria contains 71 genera and 275 species, 49.8% of which were first isolated from the marine salt environment and 50.2% from the inland salt environment, indicating that both thalassohaline and athalassohaline environments contain diverse halophilic archaea. However, there remain taxa that have not yet been isolated in pure culture, such as the nanohaloarchaea, which are widespread in the salt environment and may be one of the hot spots in the field of halophilic archaea research in the future. In this review, we focus on the cultivation strategies that have been used to isolate extremely halophilic archaea and point out some of the pitfalls and challenges.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-020-00087-3.

Polyphasic characterization of and genomic insights into a haloalkali-tolerant Saccharibacillus alkalitolerans sp. nov., that produces three cellulase isozymes and several antimicrobial compounds

A cellulase producing novel bacterial strain VR-M41^T was isolated from an open-air vegetable and fruit market. Cells are found to be rod-shaped, endospore forming, positive for Gram's stain and negative for catalase, oxidase and urease. Strain VR-M41^T was halotolerant (upto 8.0% NaCl, w/v), motile and facultative anaerobe. It grew at wide range of pH (6.0-10.0) and temperatures (20-40 °C). Strain VR-M41^T produced three isozymes of Carboxymethylcellulase. The 16S rRNA gene sequence of strain VR-M41^T was 97.3% similar to both Saccharibacillus kuerlensis DSM 22868^T and Saccharibacillus sacchari DSM 19268^T, and less than 96.4% with the rest of the valid species of the genus Saccharibacillus. Whole-genome ANI, dDDH and genome phylogenetic tree analysis revealed that strain VR-M41^T significantly differed from Saccharibacillus kuerlensis DSM 22868^T and Saccharibacillus sacchari DSM 19268^T (ANI 79.6-79.7% and dDDH 23.1%). The strain comprised of MK-7 and anteiso-C 15:0 (42.2%) as predominant isoprenoid quinone and fatty acid respectively. Major polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The draft genome of strain VR-M41^T consisted of 5,386,426 base pairs with 5103 annotated genes, out of which 2147 corresponded to hypothetical proteins and 2956 with functional assignments. Pan-genome analysis revealed the presence of 2998 core genes, 828 accessory genes, and 1131 unique genes of Saccharibacillus. Strain VR-M41^T produced antimicrobials against Staphylococcus aureus, Streptococcus pneumoniae, Micrococcus luteus and Shigella flexneri. Significant phenotypic and genotypic differentiating characteristics from closely related species, indicated that strain VR-M41^T is a novel species of the genus Saccharibacillus, for which the name Saccharibacillus alkalitolerans sp. nov., is proposed. The type strain is VR-M41^T (= KCTC 43183^T=NBRC 114337^T).