Species, Communities and Microbiomes - Vocabulary Flashcards

A set of vocabulary flashcards covering key concepts from the lecture notes on microbial species concepts, microbiomes, and community assembly.

Biological Species Concept

A group of interbreeding natural populations reproductively isolated from other such groups; individuals produce fertile offspring (actual wording varies among definitions).

• doesn’t work microbes as they do not produce sexually

Microbiome composition

• Definition: The composition of a microbiome refers to the taxonomic makeup of the microbial community in a given environment.

• Core vs. Transient Members:

  • Core microbiome = taxa consistently present across similar environments or hosts.

  • Transient microbiome = taxa that appear temporarily, influenced by season, disturbance, or chance.

• Factors shaping composition: environment (pH, nutrients, oxygen), host biology (immune system, genotype), and ecological processes (selection, dispersal, drift, diversification).

In short: microbiome composition answers “Who is there, and in what proportions?”

 

Microbiome Function

• Definition: The collective activities and roles performed by the microbiome, often more important than which species are present.

• Examples of Functions:

  • Biogeochemical cycling – nitrogen fixation, carbon degradation, sulfur reduction.

  • Nutrient exchange – microbes make nutrients available to plants or hosts.

  • Metabolite production – vitamins, antibiotics, signaling molecules.

  • Defense and stability – protection against pathogens, functional redundancy.

  • Ecosystem services – soil fertility, water purification, gut health.

• Functional Redundancy: Multiple taxa can perform the same function (e.g., several bacterial groups can degrade cellulose). This makes microbiomes resilient: even if species composition changes, function may remain stable.

• Dysfunction: Loss of diversity or disturbance can impair function (e.g., reduced nutrient cycling in degraded soils, gut dysbiosis in disease).

species in microbial ecology

The Challenge of Defining Microbial Species

• Unlike animals or plants, many microbes reproduce asexually and exchange genes horizontally.

• This makes classical definitions (e.g., biological species concept) problematic.

• Microbial species are often defined operationally using:

  • 16S rRNA similarity (>97%) – widely used but limited in resolution. We will discuss more about this during the next lecture!

  • Average Nucleotide Identity (ANI) (~95%) – genomic threshold for species-level separation.

  • Pangenome analyses – highlight that microbes share a core set of genes but also possess variable accessory genes critical for adaptation (e.g., in E. coli, ~2000 core vs. >18,000 pangenome genes).

• For fungi, species delimitation often combines morphology, multi-locus phylogenetics, ecology, and genomics.

• The definition of microbial species is context-dependent and best understood as genetically cohesive but dynamic populations shaped by both vertical inheritance and horizontal gene exchange.

Reproductive isolation

Barriers that prevent gene flow between populations, helping define species boundaries.

microbiome concept

characteristic microbial community in a habitat, its theatre of activity

• later definition shifted between ecological, host-focused, and genomic interpretations

• controversies : should phages, relic DNA, and plasmids be included? ( yes in microbiome, no in microbiota)

• microbes are dynamic in space and time

• new frameworks emphasize networks and keystone species, using multi-omics and modeling to link taxonomy to function

• community ecology provides the analytical toolkit: diversity, interactions, emergent properties ( provide tools to study microbes)

• microbiome research expands the concept to holistic systems, incorporating hosts, environment, molecules, and dynamics ( help understand how microbes work)

  Together they show :

• microbial communities aren’t just “who is there”, but what they do, how they interact, and how they respond to change

• the microbiome concept integrates ecology,evolution, and applied sciences ( medicine, agriculture, climate)

• Microbiota = the living microbial members (bacteria, archaea, fungi, protists).

• Microbiome = microbiota plus their theater of activity (environment, interactions, metabolites, mobile elements, phages, plasmids, relic DNA).

• Microbiomes are dynamic in space and time: with core members (stable, persistent) and transient members(appear only under certain conditions).

• The organisms themselves.

• The genes they carry (the community metagenome).

• The products they make (metabolites, enzymes, toxins, signaling molecules).

• Their interactions with each other (competition, cooperation, predation).

• Their interactions with the environment (soil, plant roots, the human gut).

 

Genetic Species Concept

A concept equating species with genetically cohesive lineages; sometimes called the genetic species concept

phylogenetic species concept

a species is the least inclusive taxon recognized in a formal phylogenetic classification. as will all hierarchical levels of taxa in such a classification, organisms are grouped into species because of evidence of monophylly. taxa are ranked as species rather than at some higher level because they are the smallest monophyletic groups deemed worthy of formal recognition, because of the amount of support for their monophyly and/or because of their importance in biological processes operating on the lineage in question

• works on microbes; based on DNA sequencing

Recognition Species Concept

A concept where species are defined by mate recognition systems that allow successful reproduction.

Reproductive Competition

A concept focusing on the role of reproductive barriers and competition in shaping species boundaries.

Ecological Species Concept

A lineage occupying an adaptive zone minimally different from any other lineage in its range and evolving separately (Van Valen 1976).

• doesn’t necessarily work for microbes; focuses on ecology more than evolution

Evolutionary Species Concept

A species is a lineage evolving separately from others with its own evolutionary trajectory.

General Lineage Species Concept

A species is a population lineage that has its own evolutionary fate and history.

Morphological Species Concept

Species are the smallest groups consistently and persistently distinct and diagnosable by ordinary morphology.

biome

a reasonably well defined habitat which has distinct bio-physio-chemical properties

Phenetic Species Concept

A concept based on overall similarity (phenetics), often using morphological characters.

Phylogenetic Species Concept (monophyly version)

Species are the smallest monophyletic groups with evidence of shared ancestry.

Microbes species problem

Microbes pose challenges for species definitions due to lack of sexual reproduction, horizontal gene transfer, and morphological plasticity.

Pangenome

The full complement of genes within a clade, including core and accessory genes.

• accessory genes ( virulence, niche adaptation ) frequently exchanged

• problem: phenotype doesn’t always map onto genotype

Core genome

Genes shared by all members of a clade or species.

Accessory genome

Genes present in some members but not all; often linked to virulence and niche adaptation.

Horizontal Gene Transfer (HGT)

Movement of genetic material between organisms other than vertical inheritance.

16S rRNA similarity (>97%)

A widely used operational threshold for bacterial species delineation; limited in resolving some groups.

ANI (~95%)

Average Nucleotide Identity; a robust but somewhat arbitrary genomic threshold for species delineation.

• how much of genotype is similar at nucleotide level

• doesn’t work well because values are an arbitrary threshold- no biological reason for 95% value

Operational definitions

Practical, non-universal criteria used to define microbial species in different contexts.

Microbiota

The living members of a habitat (bacteria, archaea, fungi, protists).

Microbiome

Microbiota plus their environment, interactions, structural elements, metabolites, and genetic material.

• interactions can occur at microns ( biofilms, rhizosphere hotspots) or meters ( chemical gradients in sediment)

• community defined by ecologist perspective than strict boundarieies

• community : assemnlage of species living together, interacting in a contiguous environment

Habitat generalist

A microbe with metabolic flexibility and tolerance allowing survival across multiple habitats.

Habitat specialist

A microbe adapted to a specific habitat or niche, with limited tolerance to other conditions.

Keystone species

Species whose presence has a disproportionate effect on ecosystem function relative to abundance.

Community

An assemblage of species living together in a habitat; boundaries can be fuzzy in microbes.

Selection (community assembly)

Environmental filters and biotic interactions that determine which taxa persist.

• if organism not fit for environment = death

Dispersal (community assembly)

Movement of microbes across space; facilitated by vectors and dormancy, reducing barriers.

Diversification

Emergence of new lineages through mutation, recombination, and horizontal gene transfer.

Drift

Random demographic fluctuations that alter relative abundances, independent of traits or environment.

Alpha diversity

Within-community diversity measures: richness, evenness, and phylogenetic diversity.

Beta diversity

Between-community diversity; turnover of taxa across habitats or gradients.

Gamma diversity

Regional diversity; cumulative diversity across landscapes.

Weighted UniFrac

A phylogenetic beta-diversity metric that incorporates branch lengths and taxa abundances.

Distance-decay

The decrease in community similarity as geographic distance increases.

What is a species?

> 30 species recognition critieria

• more than 30 ways to identify species and they are not all comprehensive

• bacterial species are best seen as genetically cohesive populations shaped by both vertical inheritance and HGT

• fungi=combine morphology + multi locus phylogeny + ecology + genomics

• bacteria = focus on genomic cohesion vs. HGT

species problem for microbes

• no sexual reproduction

• HGT occur between cells

• morphology alone can be misleading

• hybridization

• different evolutionary dynamics than animals/plants

• # of species described < # of species that actually exist

• pangenome structure: core genes + accessory genes ( nothing to compare microbe to)

key aspects of community ecology in microbes

functional pathways : biogeochemical transformations, resource flows

Interactions: competion, syntrophy, cross-feeding, allelopathy, signaling, HGT

emergent properties: diversity, functional redundancy, stability/resilience, community metagenome

Microbial Community assembly and diversity

• microbial communities are not random collections of species- they are shaped by ecological and evolutionary processes

• understanding these processes helps elucidate community structure and dynamics. ( explains patterns of diversity, predict ecosystem functioning, and guide applications (agriculture,medicine, conservation)

homogenous selection

selection in 2 environments generate same community

heterogenous selection

selection in 2 different environments generates distinct communities

homogenizing dispersal

communities that are closer together

• the process where a high rate of organism movement between geographically seperated communities leads to an increase in their composition similarityis known as homogenizing dispersal, which can reduce biodiversity and make ecosystems more alike.

priority effect

refers to the influence of the order of species arrival on community structure, where earlier species can affect the establishment and success of later-arriving species.

dispersal limitation

the restriction of species movement due to barriers such as geographical features or ecological factors that prevent organisms from reaching suitable habitats.

• hard to colonize microbiomeor habitats that hinder species establishment.

core processes of community assembly

these processes do not act in isolation, dispersal brings new taxa, but selection decided who survives

importance varies by spatial and temporal scales : drift may dominate in small populations, while selection drives long-term patterns

abundance distributions

most microbial communities have many rare taxa

biogeography

microbes show distance-decay patterns, but dispersal potential and dormancy alter these compared to plants/animals

phylogenetic structure

clustering often signals strong environment selection; overdispersion may reflect competiton or niche partitioning

implications for ecosystem function

• high diversity can buffer ecosystems ( functional redundancy)

• system stable to disturbance, if some die others can perform same function ( function preservation)

• assembly processes shape not just who is there but also ecosystem resilience and services

communities

• Assemblages of species living and interacting in a shared environment.

• In microbes, boundaries can be very fine (biofilms, rhizosphere hotspots) or broad (sediment layers).

• Communities can be defined from different perspectives:

  • Phenomenological community – microbes that co-occur in a space.

  • Indexical community – microbes interacting around a key process or host.

community ecology

studies how groups of organisms live together, interact, and shape ecosystems. The microbiome concept builds directly on these ecological foundations:

1. Communities as Assemblages of Species

   • In classic ecology, a community is the collection of species that coexist in a niche.

   • In microbial ecology, the microbiome represents that community but expands it to include molecular and functional dimensions.

2. Emergent Properties

   • Communities have collective traits that cannot be understood by studying single species in isolation.

   • In microbiomes, these emergent properties include diversity, stability, resilience, functional redundancy, and ecosystem services (like nutrient cycling).

3. Ecological Processes

   • Microbial community assembly follows the same processes as any other ecological community: selection, dispersal, diversification, drift.

   • The microbiome framework highlights that these processes not only determine “who is there” but also influence metabolic functions (e.g., nitrogen fixation, pathogen suppression).

4. Dynamics in Space and Time

   • Just like plant or animal communities, microbiomes are not static. They change seasonally, with disturbances, or across habitats (e.g., soil → root → leaf).

Diversity in microbial communities

Alpha Diversity (within-community diversity)

Alpha diversity refers to the diversity within a single community or sample.
It tells us how many different kinds of microbes are present (richness) and how evenly they are represented (evenness).

• Richness = number of species (or OTUs/ASVs).

• Evenness = whether species are equally abundant or dominated by a few.

• Indices like the Shannon index or Simpson index combine richness and evenness into a single number.

• Beta Diversity (between-community diversity)

  Beta diversity measures differences in community composition between two or more communities.
  It answers the question: How similar or different are these microbial communities?

  • If two samples share many of the same species, their beta diversity is low (they are similar).

  • If they share few species, their beta diversity is high (they are different).

why does microbial diversity matter?

• Diversity links to ecosystem function:

  • More taxa = broader metabolic potential.

  • Functional redundancy = stability under disturbance.

Studying microbial diversity is essential because microbes are the foundation of nearly all ecosystems, driving processes such as nutrient cycling, primary production, and decomposition. High microbial diversity often means greater functional redundancy, which provides stability and resilience when ecosystems face disturbances like climate change, pollution, or disease. Understanding diversity also helps us link community composition to ecosystem services—for example, how soil microbial diversity supports plant growth, or how gut microbiome diversity influences human health.

selection

• Environmental filters (e.g., pH, temperature, oxygen, host immunity) and biotic interactions (competition, mutualism, predation) determine which taxa persist.

• Strongly deterministic process: selects for the “best fit” organisms.

• Have a look at the figure below (panel A), selection is divided into:

  • Homogeneous selection

    • Occurs when the same environmental pressures act across sites.

    • This leads to communities that are more similar to each other than expected by chance.

    • Example: if multiple soils have the same pH and nutrient profile, they will tend to favor the same microbial taxa, resulting in convergent communities.

  • Heterogeneous selection

    • Occurs when different environmental pressures act in different sites.

    • This produces communities that are more different from each other than expected by chance.

    • Example: one soil is acidic and nutrient-poor, another is alkaline and nutrient-rich → each favors different sets of microbes, increasing beta diversity.

dispersal

• Movement of microbes across space (via water, air, soil particles, hosts).

• Microbes disperse more easily than macroorganisms, but dispersal limitation still matters (e.g., geographic differences in soil microbiomes).

• Have a look at the figure below (panel B), dispersal is divided into:

  • Homogenizing Dispersal

    • Happens when dispersal rates are very high.

    • Microbes move so freely between sites that communities become very similar, regardless of local environmental conditions.

    • Think of it as constant “mixing” that overrides local differences.

    • Example: In a river, water flow can continuously shuffle microbial cells downstream, making communities at different points look alike.

  • Priority Effects

    • Occur when the order of species arrival influences which community forms.

    • Early colonizers can modify the environment (positively or negatively) in ways that affect later arrivals.

    • This creates historical contingency: two sites with the same conditions may end up with different communities simply because colonizers arrived in a different sequence.

    • Example: In the gut of a newborn, whichever microbes colonize first can shape the long-term microbiome by occupying niches or altering pH.

  • Dispersal Limitation

    • Happens when dispersal rates are very low.

    • Microbes cannot reach all suitable habitats, so communities differ because some taxa are absent by chance.

    • This creates high beta diversity between sites, even if conditions are similar.

    • Example: Isolated soil patches may harbor unique microbial communities simply because not all microbes can travel there.

diversification

• Refers to the evolutionary generation of new genetic and functional variation within microbial lineages.

• Occurs through mutation, recombination, and horizontal gene transfer.

• Diversification creates new taxa or strains, increasing local richness and potentially altering community function.

• Example: In a long-term soil community, bacteria may acquire genes for antibiotic resistance or for metabolizing a new carbon source, creating new ecotypes that expand diversity.

drift

• Refers to random changes in species abundances due to chance events, not because of environmental selection.

• Strongest in small populations or during disturbances/bottlenecks.

• Drift can lead to the loss of rare taxa or unpredictable shifts in community composition.

• Example: If only a few microbial cells survive a drought or antibiotic treatment, the post-recovery community may differ just by chance, even if the environment hasn’t changed.

Integration:
Community structure at any time is the outcome of selection, dispersal, diversification, and drift acting together. Their relative importance changes across spatial and temporal scales.

edaphic similarity

• how alike (soil) niches are in their properties (e.g., pH, texture, organic matter, nutrients, moisture). Edaphic refers to soil, but these concepts can be applied to other ecological niches.

community similarity

how alike microbial communities are in composition (measured by beta diversity).

deterministic processes ( selection)

• Communities are strongly shaped by environmental filtering.

• Prediction:

  • When soils are edaphically similar → communities are also similar (low beta diversity).

  • When soils are edaphically different → communities diverge (high beta diversity).

  • This applies to both community composition and function.

• Example: Two soils with similar pH and organic matter host similar bacterial taxa; a very acidic soil vs. an alkaline soil select very different communities (and function).

stochastic processes ( drift, dispersal limitations)

• Community composition is shaped more by chance events or dispersal barriers than by soil properties.

• Prediction:

  • Even if soils are edaphically similar, communities may still be different because of random colonization, drift, or dispersal limitation.

  • Edaphic similarity has weaker predictive power.

  • However, when looking at function, we can observe that edaphic and function similarity correlate.

• Example: Two identical agricultural plots may harbor different microbial communities simply because different microbes arrived first (priority effects) or because rare taxa were lost by drift. However, these microbial communities, although different in composition, might perform the same function.