NATURE AND APPLICATIONS OF MICROBIAL ECOLOGY

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Arizaldo E. Castro, MSc
1
Microbial Ecology of Terrestrial and Aquatic Systems (METAS) Laboratory, Institute of Biology,
College of Science, University of the Philippines Diliman
aecastro@up.edu.ph, arizaldoc@yahoo.com

INTRODUCTION
Microbial ecology focuses on an environment’s influence to the diversity, distribution, and abundance of
different microbes (Youssef, Couger, McCully, Criado, and Elshahed, 2015). Physical and chemical factors, as well as
biological constraints, shape the structure and composition of microbial communities that inhabit natural and built
environments. Microbial ecology includes the study of topics and questions that deal with individual cells (planktonic)
to complex systems (microbial communities) that are usually composed of different microbial species. With the advent
of Next Generation Sequencing (NGS), microbial ecology faces the contemporary challenge of establishing a firm
theoretical foundation in order to efficiently organize and utilize large amounts of data that can be used to study the
diversity and evolutionary history of microbes in different environments (Barton and Northup, 2011). Two units of
analyses that can be used in addressing microbial ecology questions are niches and microbial interactions. Microbial
communities are adapted to specific environmental conditions that allowed members to functionally associate with one
another. Microbial communities may assumed niches within normal physiological conditions or extreme ones
(Rampelotto, 2013). At the microbial community level, various types of social interactions occur, which are responsible
for survival and ultimately for stable associations among microbial members. Interactions between microbial community
members may be categorized according to the consequences produced. Positive interactions, characterized by the
absence of harm inflicted to any of the interacting microbial species, include mutualism, synergism, and commensalism.
On the other hand, negative interactions include predation, parasitism, amensalism, and competition (Tshikantwa, Ullah,
He, and Yang, 2018). With the emerging methods and analytical frameworks that employ nucleotide sequence data, our
understanding of microbial ecology in different settings is becoming exponential.

BODY
Microbial communities and extreme ecosystems where they can exist
Diverse microbial communities can be hosted by various ecosystems. Microbial ecology of extreme aquatic and
terrestrial systems such as alkaline hot springs (Rozanov, Bryanskaya, Ivanisenko, Malup, and Peltek, 2017) and soil
exposed to volcanic gas emissions (Fujimura et al., 2016) can be studied by a combination of metagenomics, functional
assessment, and evaluation of environmental parameters. In a baseline study by Rozanov and colleagues (2017),
microbial community diversity and structure of a microbial mat from the Garga hot spring was analyzed using 16S rRNA
metagenomic sequencing and phylogenetic analysis. The authors report that there is high diversity and potential novelty
of Archaea in the thermal water exit of the study site. In addition, the researchers were able to stratify the analyzed
microbial mat and identify dominant species in each stratum. Cyanobacteria were found to be dominating the top layer
while facultative aerobes/microaerobes and nitrogen-fixers like Planctomycetes and Chloroflexi were found to be the
most abundant in the middle layer. On the other hand, obligate anaerobes such as species from Clostridium and
Firmicutes were found to be dominating the bottom layer of the microbial mat. These bottom-dwelling bacterial groups
are known to reduce compounds containing sulfur. With their findings on community diversity and structure, Rozanov
and colleagues (2017) were able to infer a putative scheme of how the Garga hot spring microbial mat members facilitate
flow of substance and energy. Assessments similar to this study contribute preliminary information on the microbial
community diversity of natural resources and are useful in designing follow-up research studies. Another case study of
microbial ecology in extreme environments is a comprehensive research by Fujimura and colleagues (2016). The authors
employed metagenomic analysis and functional gene abundance assessment to be able to describe the mechanisms of
microbial succession in soil substrates that are affected by long-term exposure to sulfur dioxide (SO2) emitted by Mt.
Oyama. The authors found out that autotrophic iron-oxidizing bacteria particularly Leptospirillum ferrooxidans and
Acidithiobacillus ferrooxidans, served as members of pioneer communities in sites affected by SO2. Shifts in microbial
community structure and diversity were attributable to these bacterial species that facilitated carbon dioxide (CO2) and
nitrogen (N2) fixation that led to nutrient enrichment of the soil substrate. The authors hypothesized that the eventual
decline in SO2 led to the decreased abundance of iron-oxidizers and the subsequent takeover by heterotrophic bacterial
communities (Fujimura et al., 2016). Coupling metagenome-based community diversity and structure evaluation with
function analysis is a very informative approach in modeling microbial community succession not only in extreme
environments but also in normal physiological set-ups. Both case studies underscore the importance of niche-specific
microbial communities for the execution of ecosystem services such as nutrient cycling and energy flow.

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Microbes and their interactions with animals and plants
A research topic under microbial ecology that currently draws tremendous attention from the scientific
community is how microbes interact not only with other microbes but also with potential hosts. As pathogens, microbes
usually prefer a specific host to infect and sequester nutrients from. One study by Ji, Wang, Zhao, Zai, and Li (2020)
dealt with microbe and animal interactions primarily the phylogeny and emergence of the 2019 novel coronavirus (2019-
nCoV). The authors analyzed the phylogeny and host biology of the 2019-nCoV using a recent Betacoronavirus sequence
data and 271 other corononavirus genomes. Through comprehensive sequence analysis and evaluation parallel with
assessment of relative synonymous codon usage bias of potential vertebrate hosts of the 2019-nCoV, the authors deduced
that snakes are the most likely wildlife reservoir of the virus. Phylogenetic analysis using a background of other
coronavirus sequences from different parts of the world revealed that the 2019-nCoV forms a distinct clade and together
with two bat coronaviruses, they form a monophyletic group. From the results of their findings, the authors inferred that
the 2019-nCoV is a recombinant virus between a bat coronavirus and a coronavirus of unknown origin. Further
recombination analyses led the authors to hypothesize that modifications occurring in the glycoprotein spike enabled
2019-nCoV transmission from wildlife reservoir to humans. Rapid response studies like this serves as a narrative on the
importance of understanding microbial ecology of infectious agents in cases of international public health emergencies.

Another group of microbes known to cause infection to higher order organisms is the microfungi, i.e., yeasts
and microscopic fungi. In a study by Cai and colleagues (2018), the mechanism by which mobile small RNAs (sRNAs)
from plants are transferred to fungal pathogens was elucidated by identifying the molecular effectors that facilitate the
process. Using the Arabidopsis-Botrytis pathosystem, Cai and colleagues (2018) provided multiple layers of evidence
supporting the hypothesis that sRNAs targeting pathogen virulence genes are selectively transferred from Arabidopsis
cells (plant/host) to Botrytis cells (microbe/pathogen) via plant secreted exosome-like vesicles that are associated to
Arabidopsis TETRASPANIN-like genes. From the results of sRNA profiling of control and experimental groups, the
authors discovered that sRNA transfer from plant host to fungal pathogen is not concentration-dependent. The transfer
of host sRNAs is facilitated by TET8-TET9-associated exosome-like plant vesicles that are derived from Multivesicular
Bodies (MVBs). During fungal infection, MVBs fuse with plant plasma membrane to release sRNA-containing
exosomes in the site of the infection. Fungal cells take up these sRNA-containing exosomes. The last part of the proposed
mechanism theorizes whether transferred sRNAs affect fungal virulence. By infecting triple mutant hosts that are not
capable of producing the identified pathogen-associated sRNAs, the authors observed that the susceptibility of triple
mutant hosts increased compared to the wild type as indicated by differences in lesion size and decreased accumulation
of host-transferred sRNAs in fungal protoplasts. Considering the process by which sRNAs induce their effect, an
expected downregulation of fungal target genes was seen. These pathogen genes impaired by the host sRNAs were
further verified by the authors to be involved in fungal virulence as genes that are associated to vesicle-trafficking (Cai
et al., 2018). Both case studies explored microbe-host interactions. In this context, interactions are said to follow the
Zig-Zag model of host/plant-pathogen interaction proposed by Jones and Dangl (2006). These studies support the
usefulness of nucleotide sequence data in understanding how specific interactions in host-pathogen systems occur as
well as in shedding insights about the evolution/speciation of new infectious microbes.

Microbe-microbe interactions in artificial environments

In natural settings, most microbial species exist in communities associating and interacting with one another. In
the human body, communities of microbes are known to be present in regions such as the gut where they facilitate
biological and chemical processes. The nature of these interactions at the microbial environment level is a focal topic in
microbial ecology. In a study by Gutierrez and Garrido (2019), emerging microbe-microbe interactions in the context of
an artificial environment were studied. 14 bacterial species known to co-exist in the human gut were artificially
constructed as a microbial consortium fed with inulin. Utilizing species deletion as an experimental approach in
understanding the effects produced by the absence of a specific bacterium in their constructed consortium, the authors
were able to unravel emerging interactions. They were able to identify Bacteroides dorei as a keystone bacterium
important for carbohydrate and short chain fatty acid metabolism in the gut as supported by the results of the study. By
looking into substrate consumption, microbial community composition, and metabolite production, the authors were
able to generalize the importance of certain bacterial species for the survival and promotion of others, e.g.,
Lachnoclostridium symbiosum’s ability to produce butyrate was promoted by co-existing bacterial species such as
Escherichia coli, Lactobacillus plantarum, Bifidobacterium adolescentis, and B. dorei. This study demonstrates that
studying microbe-microbe interactions will require capturing the multiple dimensions of such interactions namely effects
on microbe abundance, on byproduct formation, and on microbial community structure. Furthermore, assessments of
microbial communities in artificial settings are useful in designing microbial associations and interactions that are
optimized to carry out a desired function, e.g., secondary metabolite synthesis, breakdown of large biomass substances,
etc.

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CONCLUSION
Studying microbial communities with the goal of understanding their evolutionary and ecological dynamics has
become inevitably high-resolution. The employment of indirect culture-independent methods such as metagenomics
and genotype- and phenotype-based function analyses revolutionized how microbial interactions and niches should be
explored and theorized. We are currently recognizing that microbial communities in natural ecosystems and built
environments are indeed functionally diverse and this opens a growing list of research topics and questions under the
purview of microbial ecology. These functionally diverse microbes and microbial communities have potential
applications for the resolution of current human challenges, i.e., mitigating the effects of climate change, ensuring food
security, and improving human health amidst infectious and non-infectious diseases.

The wealth of microbial ecology data we are collecting from ecosystems and artificial settings is expected to
grow exponentially and will eventually need a firm framework that marries macroecology with microecology. This
framework must be able to integrate quantitative and qualitative dimensions of variables that are assessed in microbial
ecology studies. In prospect, capturing the diversity, abundance, and functions of microbial communities will require
not only the use of nucleotide sequence data but also datasets on various characteristics of microbial communities, i.e.,
substrate consumption/preference, community succession/structural changes, and emerging social interactions.

Aside from a unifying research framework, there is also a need for increased scientific visibility of
computational tools and processes used in analyzing genomic and metagenomic data. Democratized access to these
tools will allow microbial ecology analyses that are comparable across regions of the world. These initiatives and their
successful implementation will ensure that microbial ecology will assume a progressive and future-proof form that
churns out knowledge and information necessary to understand microbial communities and the bigger role they play in
the whole of the biosphere.

REFERENCES
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Cai, Q., Qiao, L., Wang, M., He, B., Lin, F. M., Palmquist, J., Huang, S. D., & Jin, H. (2018). Plants send small
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Fujimura, R., Kim, S. W., Sato, Y., Oshima, K., Hattori, M., Kamijo, T., & Ohta, H. (2016). Unique pioneer
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Gutiérrez, N., & Garrido, D. (2019). Species Deletions from Microbiome Consortia Reveal Key Metabolic
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Ji, W., Wang, W., Zhao, X., Zai, J., Li, X. (2020). Cross-species transmission of the newly identified coronavirus
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Jones, J., Dangl, J. (2006). The plant immune system. Nature 444, 323–329.
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Rampelotto P. H. (2013). Extremophiles and extreme environments. Life (Basel, Switzerland), 3(3), 482–485.
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Rozanov, A. S., Bryanskaya, A. V., Ivanisenko, T. V., Malup, T. K., & Peltek, S. E. (2017). Biodiversity of the
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