Complete genome sequence of the endophytic bacterium Cellulosimicrobium sp. JZ28 isolated from the root endosphere of the perennial desert tussock grass Panicum turgidum

Comparative genomic characterization of Cellulosimicrobium funkei isolate RVMD1 from Ma'an desert rock varnish challenges Cellulosimicrobium systematics

Desert environments harbor unique microbial communities. This study focuses on Cellulosimicrobium funkei isolate RVMD1, isolated from rock varnish in the Ma'an Desert. Initial identification was achieved using 16S rRNA gene sequencing, followed by whole-genome sequencing (WGS) for comprehensive characterization. The genome comprises 4,264,015 base pairs (857 contigs) with a high G + C content of 74.59%. A total of 4,449 proteins were predicted. Comparative analysis utilizing OrthoANI, ANI, AAI, and dDDH metrics suggests that RVMD1 belongs to the C. cellulans group, with the highest similarity to C. funkei (97.71% ANI). Phylogenomic analysis of 43 Cellulosimicrobium genomes revealed significant heterogeneity within the genus. Our results challenge current systematics, with C. cellulans potentially representing up to 9 distinct genomospecies. Isolate RVMD1 shows genetic adaptations to its desert environment, including genes for denitrification, oxygen and sulfur cycling, and diverse hydrogen metabolism. Pangenomic analysis uncovered a considerable number of unique genes within RVMD1, highlighting its genetic distinctiveness. Gene family expansions suggest evolution in response to stressors like UV radiation and nutrient limitation. This study represents the first whole-genome analysis of a bacterium isolated from Jordanian rock varnish, emphasizing the value of WGS in understanding microbial diversity and adaptation in extreme environments.

Atacama desert actinomycetes: taxonomic analysis, drought tolerance and plant growth promoting potential

This study was designed to recover representative culturable actinomycetes from the Atacama Desert, and to detect their ability to promote plant growth under drought conditions. Environmental samples were taken from three Atacama Desert habitats, namely, from the Aguas Calientes, Lomas Bayas and Yungay core regions. With one exception higher actinomycete counts were obtained when isolation media were inoculated with mineral particles than with corresponding aliquots of serial dilution. Comparative 16S rRNA gene sequencing showed that representative isolates belonged to thirteen genera including putative novel Blastococcus, Kocuria, Micromonospora, Pseudonocardia, Rhodococcus and Streptomyces species. Representative isolates produced indole-3-acetic acid, siderophore and solubilized phosphate as well as displaying an ability to grow under drought conditions. In conclusion, the current findings open up exciting prospects for the promising potential of actinomycetes from the Atacama Desert to be used as bioinoculants to promote plant growth in arid and semi-arid biomes.

Advancement in the molecular perspective of plant-endophytic interaction to mitigate drought stress in plants

Change in global climate has started to show its effect in the form of extremes of temperatures and water scarcity which is bound to impact adversely the global food security in near future. In the current review we discuss the impact of drought on plants and highlight the ability of endophytes, microbes that inhabit the plants asymptomatically, to confer stress tolerance to their host. For this we first describe the symbiotic association between plant and the endophytes and then focus on the molecular and physiological strategies/mechanisms adopted by these endophytes to confer stress tolerance. These include root alteration, osmotic adjustment, ROS scavenging, detoxification, production of phytohormones, and promoting plant growth under adverse conditions. The review further elaborates on how omics-based techniques have advanced our understanding of molecular basis of endophyte mediated drought tolerance of host plant. Detailed analysis of whole genome sequences of endophytes followed by comparative genomics facilitates in identification of genes involved in endophyte-host interaction while functional genomics further unveils the microbial targets that can be exploited for enhancing the stress tolerance of the host. Thus, an amalgamation of endophytes with other sustainable agricultural practices seems to be an appeasing approach to produce climate-resilient crops.

Actinobacteria From Desert: Diversity and Biotechnological Applications

Deserts, as an unexplored extreme ecosystem, are known to harbor diverse actinobacteria with biotechnological potential. Both multidrug-resistant (MDR) pathogens and environmental issues have sharply raised the emerging demand for functional actinobacteria. From 2000 to 2021, 129 new species have been continuously reported from 35 deserts worldwide. The two largest numbers are of the members of the genera Streptomyces and Geodermatophilus, followed by other functional extremophilic strains such as alkaliphiles, halotolerant species, thermophiles, and psychrotolerant species. Improved isolation strategies for the recovery of culturable and unculturable desert actinobacteria are crucial for the exploration of their diversity and offer a better understanding of their survival mechanisms under extreme environmental stresses. The main bioprospecting processes involve isolation of target actinobacteria on selective media and incubation and selection of representatives from isolation plates for further investigations. Bioactive compounds obtained from desert actinobacteria are being continuously explored for their biotechnological potential, especially in medicine. To date, there are more than 50 novel compounds discovered from these gifted actinobacteria with potential antimicrobial activities, including anti-MDR pathogens and anti-inflammatory, antivirus, antifungal, antiallergic, antibacterial, antitumor, and cytotoxic activities. A range of plant growth-promoting abilities of the desert actinobacteria inspired great interest in their agricultural potential. In addition, several degradative, oxidative, and other functional enzymes from desert strains can be applied in the industry and the environment. This review aims to provide a comprehensive overview of desert environments as a remarkable source of diverse actinobacteria while such rich diversity offers an underexplored resource for biotechnological exploitations.

A genomic perspective on the potential of termite-associated Cellulosimicrobium cellulans MP1 as producer of plant biomass-acting enzymes and exopolysaccharides

Background

Lignocellulose is a renewable and enormous biomass resource, which can be degraded efficiently by a range of cocktails of carbohydrate-active enzymes secreted by termite gut symbiotic bacteria. There is an urgent need to find enzymes with novel characteristics for improving the conversion processes in the production of lignocellulosic-based products. Although various studies dedicated to the genus Cellulosimicrobium as gut symbiont, genetic potential related to plant biomass-acting enzymes and exopolysaccharides production has been fully untapped to date.

Methods

The cellulolytic bacterial strain MP1 was isolated from termite guts and identified to the species level by phenotypic, phylogenetic, and genomic analysis. To further explore genes related to cellulose and hemicellulose degradation, the draft genome of strain MP1 was obtained by using whole-genome sequencing, assembly, and annotation through the Illumina platform. Lignocellulose degrading enzymes and levan production in the liquid medium were also examined to shed light on bacterial activities.

Results

Among 65 isolates obtained, the strain MP1 was the most efficient cellulase producer with cellulase activity of 0.65 ± 0.02 IU/ml. The whole genome analysis depicted that strain MP1 consists of a circular chromosome that contained 4,580,223 bp with an average GC content of 73.9%. The genome comprises 23 contigs including 67 rRNA genes, three tRNA genes, a single tmRNA gene, and 4,046 protein-coding sequences. In support of the phenotypic identification, the 16S rRNA gene sequence, average nucleotide identity, and whole-genome-based taxonomic analysis demonstrated that the strain MP1 belongs to the species Cellulosimicrobium cellulans. A total of 30 genes related to the degradation of cellulases and hemicellulases were identified in the C. cellulans MP1 genome. Of note, the presence of sacC1-levB-sacC2-ls operon responsible for levan and levan-type fructooligosaccharides biosynthesis was detected in strain MP1 genome, but not with closely related C. cellulans strains, proving this strain to be a potential candidate for further studies. Endoglucanases, exoglucanases, and xylanase were achieved by using cheaply available agro-residues such as rice bran and sugar cane bagasse. The maximum levan production by C. cellulans MP1 was 14.8 ± 1.2 g/l after 20 h of cultivation in media containing 200 g/l sucrose. To the best of our knowledge, the present study is the first genome-based analysis of a Cellulosimicrobium species which focuses on lignocellulosic enzymes and levan biosynthesis, illustrating that the C. cellulans MP1 has a great potential to be an efficient platform for basic research and industrial exploitation.

Cellulosimicrobium fucosivorans sp. nov., isolated from San Elijo Lagoon, contains a fucose metabolic pathway linked to carotenoid production

Cellulosimicrobium strain SE3^T was isolated from the San Elijo coastal lagoon near San Diego. A whole genome-based phylogenetic comparison shows great heterogeneity within the Cellulosimicrobium genus. Based on average nucleotide identity, whole genome-based comparison, and the presence of a unique L-fucose metabolic pathway, strain SE3^T was shown to belong to a novel species within the genus, together with five other strains. The name Cellulosimicrobium fucosivorans sp. nov. is proposed, with strain SE3^T as the type strain. The strain encodes a unique alpha-L-fucosidase and the L-fucose metabolic pathway is homologous to the one recently described in Campylobacter jejuni. C. fucosivorans is able to grow on L-fucose, and interestingly, the biosynthesis of the yellow carotenoid is dependent on the presence of L-fucose in the media. The ability to metabolize fucose and the linked production of carotenoids are expected to provide C. fucosivorans with a competitive advantage in the sunny coastal lagoon area.

Development of an inexpensive matrix-assisted laser desorption-time of flight mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize

Many endophytes and rhizobacteria associated with plants support the growth and health of their hosts. The vast majority of these potentially beneficial bacteria have yet to be characterized, in part because of the cost of identifying bacterial isolates. Matrix-assisted laser desorption-time of flight (MALDI-TOF) has enabled culturomic studies of host-associated microbiomes but analysis of mass spectra generated from plant-associated bacteria requires optimization. In this study, we aligned mass spectra generated from endophytes and rhizobacteria isolated from heritage and sweet varieties of Zea mays. Multiple iterations of alignment attempts identified a set of parameters that sorted 114 isolates into 60 coherent MALDI-TOF taxonomic units (MTUs). These MTUs corresponded to strains with practically identical (>99%) 16S rRNA gene sequences. Mass spectra were used to train a machine learning algorithm that classified 100% of the isolates into 60 MTUs. These MTUs provided >70% coverage of aerobic, heterotrophic bacteria readily cultured with nutrient rich media from the maize microbiome and allowed prediction of the total diversity recoverable with that particular cultivation method. Acidovorax sp., Pseudomonas sp. and Cellulosimicrobium sp. dominated the library generated from the rhizoplane. Relative to the sweet variety, the heritage variety c ontained a high number of MTUs. The ability to detect these differences in libraries, suggests a rapid and inexpensive method of describing the diversity of bacteria cultured from the endosphere and rhizosphere of maize.

Desert Microbes for Boosting Sustainable Agriculture in Extreme Environments

A large portion of the earth's surface consists of arid, semi-arid and hyper-arid lands. Life in these regions is profoundly challenged by harsh environmental conditions of water limitation, high levels of solar radiation and temperature fluctuations, along with soil salinity and nutrient deficiency, which have serious consequences on plant growth and survival. In recent years, plants that grow in such extreme environments and their naturally associated beneficial microbes have attracted increased interest. The rhizosphere, rhizosheath, endosphere, and phyllosphere of desert plants display a perfect niche for isolating novel microbes. They are well adapted to extreme environments and offer an unexploited reservoir for bio-fertilizers and bio-control agents against a wide range of abiotic and biotic stresses that endanger diverse agricultural ecosystems. Their properties can be used to improve soil fertility, increase plant tolerance to various environmental stresses and crop productivity as well as benefit human health and provide enough food for a growing human population in an environment-friendly manner. Several initiatives were launched to discover the possibility of using beneficial microbes. In this review, we will be describing the efforts to explore the bacterial diversity associated with desert plants in the arid, semi-arid, and hyper-arid regions, highlighting the latest discoveries and applications of plant growth promoting bacteria from the most studied deserts around the world.