Actinobacteria produce structurally diverse bioactive natural products, such as enzymes,
antibiotics, antitumor and immune regulatory agents. Actinobacteria are not only the
main producers of microbial-derived drugs, they also play an important role as symbionts
in plant-associated microbial communities (Barka et al., 2015). At the same time,
members of the phylum Actinobacteria were found to be widely distributed in different
ecological environments, including diverse special and extreme habitats of aquatic
and terrestrial ecosystem (Qin et al., 2011; Dhakal et al., 2017; Goodfellow et al.,
2018). Compared with actinobacteria from temperate habitats, the community structure,
diversity, biological activities, and mechanisms of environmental adaptation of those
actinobacteria in special and extreme environments are relatively unstudied and unclear,
and their functions and utilization are even less reported. These actinobacteria are
potential new sources of novel natural products and functions for exploitation in
medicine, agriculture, and industry.
It's exciting that there are more and more reports in this field recently. These discoveries
make us consider some intriguing and new questions, such as, are actinobacteria ubiquitous
in the special and extreme environment on Earth, and where are the limits of their
survival? At the same time, the discovery of more and more pure cultures and new taxa
of actinobacteria from extreme environments has raised new questions for the taxonomy
of the phylum Actinobacteria. How can we establish a more accurate taxonomic system
to reflect the natural evolutionary relationship of Actinobacteria? Moreover, how
can we recognize the specific ecological functions of these ecologically adapted actinobacteria
and their potential unique environmental adaptation mechanisms? Following the success
of the Research Topic, “Actinobacteria in special and extreme habitats: diversity,
functional roles, and environmental adaptations” (Qin et al., 2016), organized in
2015, we are happy to launch a second edition. More than 100 authors, from 14 different
countries, contributed a total of 16 articles in this new edition, including one review
paper and 15 original research articles, covering a variety of topics related to actinobacteria
in special and extreme habitats. These articles addressed issues related to the cultivation
methods of rare actinobacteria, metagenomic analyses of diversity, phylogenomic taxonomy,
genome mining, bioactive compounds, and their habitat adaptation mechanism using omics
approaches. We are grateful to all authors who have submitted their manuscripts to
the second edition of this Research Topic.
The special and extreme environments are likely to contain abundant rare actinobacteria
and novel species. However, the acquisition of pure culture is a prerequisite for
the further study of their classification and function. Caves spread all over the
world, being dark, humid, and nutrient-limited. The cultivation of these cave microorganisms
has proven to be challenging (Ghosh et al., 2017). An original article by Fang et
al. explores the effects of heat pretreatment, pH, and calcium salts on isolation
of rare actinobacteria from Karstic Caves in Yunnan, China. A total of 204 isolates
were cultured, and the authors obtained a high number of 29 different rare actinobacterial
genera. Actinobacteria from caves have been found to produce a variety of secondary
metabolites. However, studies of microbial ecology in caves are still very limited.
Recently, members of actinobacteria were reported to be possibly involved in the moonmilk
genesis (Bindschedler et al., 2014). Interestingly, the article by Maciejewska et
al. provides novel evidences that some filamentous Streptomyces could be key protagonists
in the genesis of moonmilk through a wide spectrum of biomineralization processes.
These studies enlarged our knowledge on cave actinobacterial diversity and their special
ecological functions. Desert is the most extreme non-polar biome on Earth. Recent
metagenomic analyses of hyper-arid and extreme hyper-arid desert soils revealed a
remarkable degree of actinobacterial “dark matter” (Idris et al., 2017). The diversity
of actinobacterial taxa in the Badain Jaran (BJD) and Tengger Deserts (TGD) of China
were assessed using combined cultivation-dependent and high-throughput sequencing
techniques (Sun et al.). These authors found that the phylum Actinobacteria was the
predominant, comprising 35.0 and 29.4% of the communities in the two desert sands,
respectively. Taxonomic classification of 1,162 actinobacterial strains revealed a
high diversity of 73 genera, including 37 new taxa, and 10.36 % of the tested isolates
showed antimicrobial activities (Sun et al.). However, their ecological significance
in deserts deserved further exploration.
Marine actinobacteria have attracted more and more attention because of their special
physiological characteristics and capacity of producing various natural compounds
with diverse bioactivities (Schinke et al., 2017). However, marine actinobacteria
producing anti-complement agents are still poorly explored. Xu et al. analyzed the
genome of a marine Streptomyces sp. DUT11, which showed a strong anti-complement activity,
and isolated the active compounds tunicamycins I, V, and VII. Another marine actinobacterium,
Glycomyces sediminimaris UTMC 2460, which showed anti-microfouling activity, was analyzed
for its active compounds. These authors concluded that diketopiperazines produced
by this strain could be used as environmentally safe anti-fouling agents to prevent
the fouling process in marine habitats (Heidarian et al.). The article by Sun et al.
reveals the marine adaptation mechanism of a sponge-derived actinobacterium, Kocuria
flava S43, by comparative genomics analysis. These authors found that gene acquisition
was probably a primary mechanism of environmental adaptation in K. flava S43 (Sun
et al.). These studies indicated that marine actinobacteria are rich sources of diverse
biological compounds.
In this Research Topic, we collected five papers related to endophytic actinobacteria,
which is also a research hotspot in recent years. Habitat-adapted, symbiotic, indigenous
endophytic actinobacteria from special and extreme habitats probably contain novel
taxa and compounds, and enhance their host tolerance of harsh environments (Mesa et
al., 2017; Qin et al., 2018). The article by Singh and Dubey reviews the taxonomic
and chemical diversity of endophytic actinobacteria in arid, mangrove, non-mangrove
saline and aquatic ecosystems and discusses their potential biotechnological applications.
Similarly, Jiang et al. explores the diversity and antibacterial activities of endophytic
actinobacteria from five different mangrove plants in Guangxi Zhuang Autonomous Region,
China; they found 28 actinobacterial genera and four potential new species. The two
articles by Bibi et al. and Wei et al. report on the endophytic actinobacteria and
their biological secondary metabolites from the halophyte Salsola imbricate and Chinese
tea plants; their results confirm again that endophytic actinobacteria might be an
undeveloped bioresource library for active compounds. Lasudee et al. report the actinobacteria
associated with arbuscular mycorrhizal spores of Funneliformis mosseae, and explore
their potential plant growth promotion effects in agriculture; results showed that
the isolates could produce indole-3-acetic acid (IAA) and siderophores, solubilize
phosphate, and promote rice plant growth.
Genome sequencing and the phylogenomic strategy have been explored for the research
of taxonomy and prokaryotic systematics. For instance, the class Acidimicrobiia is
comprised of few cultivable species at present, containing only the order Acidimicrobiales,
two families Acidimicrobiaceae and Iamiaceae with few genera (Ludwig et al., 2012).
Hu et al. analyzed 20 sequenced members of this class and identified 15 conserved
signature indels (CSIs) in widely distributed proteins and 26 conserved signature
proteins (CSPs); the phylogenomic analysis revealed another three major lineages in
addition to the two recognized families. Furthermore, Sangal et al. revisit the taxonomic
status of the biomedically and industrially important genus Amycolatopsis, using a
phylogenomic approach. According to the genome sequences analysis and the core genome
phylogeny, genus Amycolatopsis was subdivided into four major clades and several singletons
(Sangal et al.). These results indicate that whole genome sequencing analysis can
provide more accurate taxonomic status for prokaryotes.
The developments of omics methods have provided a robust support for our understanding
of the actinobacterial adaptation mechanisms to the special and extreme habitats.
Cornell et al. obtained 76 plasmid-containing isolates of actinomycetes from the Great
Salt Plains of Oklahoma. Eleven isolates were chosen for genome sequencing, and the
results revealed the presence of series genes involved in antibiotic production, antibiotic,
and heavy metal resistance, osmoregulation, and stress response, which likely facilitate
their survival in the extreme halophilic environment (Cornell et al.). By transcriptome
analysis, physiological, and molecular experiments, Han et al. found that accumulation
of ectoine played a vital role for the salt stress tolerance of the halotolerant Nocardiopsis
gilva YIM 90087T. The article by Yin et al. report that a hybrid strategy was used
to utilize carbon sources at different temperatures by an aerobic, and cellulose degrading
thermophilic actinomycete, Thermoactinospora rubra YIM 77501T, by using combined genomic
and transcriptomics methods.
In summary, this Research Topic second edition presents recent discoveries on diversity,
function roles, and environmental adaptations of actinobacteria in special and extreme
habitats; and broadens our knowledge of actinobacterial diversity and their ecophysiological
function. We are delighted to present this Research Topic in Frontiers in Microbiology.
We hope that readers of the Journal will not only enjoy this Research Topic but also
will find it a useful reference. Future research still looks forward to the innovation
and application of new technologies, such as the application of single cell microfluidic
technique to obtain new pure cultures. At the same time, the cooperation of different
disciplines, and international cooperation of scientists from different countries
should be strengthened. We also believe that in the future, more “dark matter” from
actinobacteria in special and extreme environments will be discovered and utilized
for the benefit of human beings.
Author Contributions
W-JL and SQ organized this topic. SQ wrote the editorial article. H-PK, WH, and IA
are co-editors of the topic and discussed the writing.
Conflict of Interest Statement
The authors declare that the research was conducted in the absence of any commercial
or financial relationships that could be construed as a potential conflict of interest.