The aim of this special issue is to emphasize on the ecology of microorganisms, the
most diverse and abundant group of organisms on Earth, and to infer on biotechnological
applications. Even though we live in a microbially dominated planet only the past
decade the study of the microbial diversity has entered a period of considerable importance
to science in general, industry, protection of the environment, and public policy
making. Environmental microbes are immensely diverse and have numerous metabolic activities
and products that could have industrial applications. This treasured reservoir is
largely unexploited since more than 99% of environmental microbes cannot be cultured
under current laboratory conditions, leaving their potential largely unused. Understanding
the unculturable fraction of Earth's microbiome is essential to understand the evolution,
sustainability of life on Earth, and the development of various industrial products
that have potential applications across all major industries.
This special issue contains seven reviews and eighteen research articles that provide
a better understanding (a) of the hidden microbial diversity and (b) the use and development
of new technologies that can lead to potential biotechnological applications.
K. A. Kormas and D. S. Lymperopoulou presented a review article on the meta-analysis
of the 16S rRNA and mlrA (microcystinase) gene diversity of isolates that are known
to degrade cyanobacterial toxins. Members of Proteobacteria, Arthrobacter, Bacillus,
and Lactobacillus have been found as potential degraders of the toxins produced by
Cyanobacteria.
S. Nikolaki and G. Tsiamis presented a comprehensive overview of the advanced tools
that became available in the last few years to the microbial ecologist and describe
recent examples and future applications of such tools including phylogenetic and functional
microarrays, next generation sequencing, and single cell genomics. These tools will
enable exploitation of the previously unknown microbial diversity in biotechnology.
O. Selama et al. attempt to correlate the presence of common bacterial phyla to geographical
regions (countries/continents) using the NCBI nucleotide database to get microbial
data accessions with a country qualifier set and compare with the global biodiversity
information facility (GBIF) database data set. This work emphasizes the importance
of metadata tracking and submission in a standardized and enforced fashion and highlights
the limitations of resources such as NCBI and GBIF as well as the biased sampling
throughout the years, which limits an unbiased understanding of bacterial biodiversity
and geographical abundance.
S. Ntougias et al. provided a detailed review of the microbial communities identified
over the past 20 years in olive mill wastes (OMW) using both culture-dependent and
culture-independent approaches. They also discuss OMW-induced toxicity and the effects
that the OMW have on soil microbiota. Finally, it is presented in an elegant way the
biotechnological importance of the OMW microbiota with respect to (a) the biodegradation
of OMWs, (b) the bioconversion aspects of the OMW microbiota, and (c) the plant-disease-suppressive
properties of OMW.
D. Trabelsi and R. Mhamdi report on the effect that the release of microbial agents
could have on indigenous soil microbial communities and provide an extensive review
on the most significant studies addressing the impact of inoculation on soil microbial
communities. The authors conclude that the assessment of the observed impacts depends
largely on the techniques used to address the dynamics of the soil microbial communities.
Three papers by L. Berg et al., A. K. Chaudhary et al., and P. Jeandet et al. add
new insights into the concept of microbial cell factories and their exploitation as
platforms for the biosynthesis of numerous molecules. The first paper describes the
application of a combinatorial mutagenetic approach, which resulted in the development
of variants of the P
AOX1
promoter of the yeast Pichia pastoris with increased expression levels and abolished
glucose repression. The second paper provides an overview of the application of omic
approaches into the engineering of Streptomyces aiming to augment their industrial
exploitation in the production of secondary metabolites. Pitfalls that have hampered
the use of Streptomyces as cell factories for the production of antibiotics are described
and current examples and future trends on the use of omics in the genetic improvement
of this Actinobacteria group are presented. The third paper gives an overview of the
recent progresses that have been made for the last 10 years in metabolic engineering
of microorganisms for the biosynthesis of natural products of pharmaceutical significance.
Two papers report on the complexity of the microbial interactions. L. Vanysacker et
al. following a multiphasic approach demonstrated the complexity of the microbial
interactions controlling biofilm formation on microfiltration membranes used in wastewater
treatment facilities. Their study elegantly demonstrated that it is mostly the composition
of the microbial community and not the type of membrane that drives the biofouling
process. C. Díaz et al. studied the behaviour of yeasts during spontaneous wine fermentation
using culture-dependent and culture-independent approaches. They report that the yeast
diversity in musts from red grape was greater than the one recorded from white grape
varieties. Interestingly, yeast quantification indicated that non-Saccharomyces yeasts
were present during the entire fermentation process with R. mucilaginosa and P. anomala
being the most prominent species.
Three papers by L. Bifulco et al., M. Stathopoulou et al., and I. Fhoula et al. report
on the exploitation of bacterial and gene diversity for the development of potential
biotechnological applications. The first paper presents a first evidence for the development
and preliminary validation of an electrochemical genosensor, which could be used as
a rapid diagnostic tool for the detection of pathogenic Listeria monocytogenes over
nonpathogenic Listeria strains. This is based on the detection of the inlA gene encoding
an 80 kDa surface protein which allows Listeria to enter the cells. The second paper
by P. Stathopoulou et al. examined the lipolytic profile of 101 bacterial strains
isolated from the volcanic area of Santorini, Aegean Sea, Greece. Nine bacterial strains
exhibiting extracellular lipase activities were characterized as Aneurinibacillus
sp. with an optimum activity at 70–80°C (pH 8-9). The isolated lipases revealed exceptional
thermostability with high optimum activity temperatures, and they represent very promising
candidate enzymes for a variety of high temperature industrial lipolytic applications.
The third paper by I. Fhoula et al. examined the biotechnological properties of lactic
acid bacteria isolated from the rhizosphere of olive trees and desert truffles. Rhizospheric
strains that belong to Enterococcus and Weissella exhibited strong antibacterial activity
against plant pathogenic and food-borne bacteria.
The papers by I. Maeda et al., C. Hamdi et al., and A. Rizzi et al. examined the diversity
of gut microbes. More specifically I. Maeda et al. present a study of gut microorganisms
from three jungle crows using 16S rRNA-targeted sequencing which reveals the presence
of potentially pathogenic bacterial genera. These findings indicate the importance
of crows in public health and their role as natural reservoirs of pathogenic microorganisms.
C. Hamdi et al. examined the diversity of Paenibacillus larvae, the causative agent
of American foulbrood (AFB). BOX-PCR fingerprints indicated relatively high intraspecific
diversity among the P. larvae isolates with six genotypes being identified. A. Rizzi
et al. characterized the gut microbial communities that are associated with the wood-boring
beetle Anoplophora chinensis using culture-dependent and culture-independent approaches.
Mainly Proteobacteria, Actibobacteria, and Firmicutes dominated the bacterial diversity
with the most dominant taxa being the Enterobacteriaceae family of Gammaproteobacteria.
Three papers by D. El Hidri et al., C Moulas et al., and L. Ma et al. studied the
diversity of microbes in different ecosystems. D. El Hidri et al. deployed a culture-dependent
approach to study the diversity and ecology of haloalkaliphilic bacteria in arid saline
ecosystems from Southern Tunisia. 122 haloalkaliphilic strains were isolated with
thirteen genera and twenty distinct species being identified. In the second paper
C. Moulas et al. examined the impact of two systemic pesticides on the epiphytic fungal
and bacterial communities via DGGE and cloning. The fungal community was dominated
by putative plant pathogenic ascomycetes, with yeast isolates of Cryptococcus sp.
being stimulated by the application of imidacloprid, suggesting a potential role in
its degradation. In the third paper the composition and dynamics of planktonic viruses
and their relationship with environmental parameters in natural freshwater were examined.
Correlation analysis indicated that the main factor influencing viral abundance is
bacteria.
Two papers by M. S. Silva et al. and G. S. Kanini et al., addressed the Actinobacterial
diversity and their potential biotechnological applications. In the first paper the
diversity of Actinobacteria spp from three Brazilian Savannah soils was examined.
All sites exhibited a high Streptomyces diversity and interestingly enough there were
no significant differences in the concentrations of phosphorus, magnesium, and organic
matter in the soils. Samples from the rainy season exhibited higher Actinobacterial
diversity than the samples from the dry season. In the second paper the bacterial
strain ACTA155, member of Streptomyces genus isolated from diverse Greek habitats,
exhibited strong antifungal activity against the phytopathogenic fungus Fusarium oxysporum.
Interestingly, the metabolites involved in the antagonistic action of the isolate
showed to be more than one and produced independently of the presence of the pathogen
which further highlighted the biotechnological potential of this isolate.
Two papers by A. Krimitzas et al. and I. B. Fekih et al. examined fungal diversity.
In the first paper the diversity of Aspergillus species using morphological and molecular
criteria is presented. In very diverse genera like Aspergillus the use of single gene-based
analyses does not solve all ambiguities and does not always represent the evolutionary
history of the species. Utilization of nuclear and mitochondrial genes enabled the
authors to fully characterize more than thirty-five Aspergillus strains in sixteen
sections. In the second paper the diversity of Entomophthoralean fungi was investigated
using morphological and molecular (ITS) markers in the aphid species of Sitobion avenae
and Entomophthora planchoniana, with the fungal species of Pandora neoaphidis and
Entomophtra planchoniana being the most dominant.
The role of plant growth promoting (PGP) bacteria was examined in two papers. R. Marasco
et al. examined the environmental factors that influence the PGP potential of the
root-associated bacteria with the grapevine root system from Egypt, Tunisia, and Northern
Italy. PCR-DGGE analysis indicated that the structure of endospheric and rhizospheric
bacterial communities was highly diverse and was associated with a cultivar/latitudinal/climatic
effect. The microbial profile of the Tunisian grapevines was more similar with the
Tunisian than those cultivated in Northern Italy. In the second paper F. Mapelli et
al. characterized halophilic/halotolerant bacteria from the rhizosphere of Salicornia
plants and bulk soil collected from hypersaline systems in Tunisia. The biotechnological
potential of these isolated bacterial strains was further highlighted when at least
twenty Halomonas strains displayed PGP features in vitro and were able to colonize
Salicornia roots under laboratory conditions.
Collectively, these papers give a comprehensive view on the immense potential that
the study of microbial diversity can provide towards the development of biotechnological
applications. Current and ongoing advances in the field of omic approaches will certainly
propel our capacity to understand and further exploit microbial diversity. In this
regard, these articles provide a prospective into the future of this field.