Microbial Planet Archive

Archive

dispatches, essays, and issue collections from Microbial Planet, organized by volume and issue

Vol. 5 Vol. 4 Vol. 3 Vol. 2 Vol. 1

Image note Some illustrations were created with AI-assisted image generation and edited or selected for Microbial Planet. Scientific text, interpretation, and citations remain author produced and curated.

Volume 5

2026

Issue 1 - CURRENT ISSUE

Summer 2026

Volume 4

2024

Issue 1

Spring 2024

Cover Feature

Foundations of Biogeochemical Cycling

This issue of Microbial Planet is adapted from material developed for Dynamic Earth II: Biogeochemical Cycles, a graduate course in the Department of Earth Sciences at Southern Methodist University (SMU). The course is built around a central question: how do energy, water, carbon, nutrients, organisms, and Earth materials interact to produce the functioning biosphere? Rather than treating biogeochemical cycles as static diagrams of elemental movement, the course emphasizes fluxes, transformations, feedbacks, and constraints across the atmosphere, hydrosphere, lithosphere, and biosphere.

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In This Issue

Dispatches and related readings

Biogeochemistry

Evolution of the Biosphere

Earth history is often divided by geology, but much of that history was shaped by biology. For more than three billion years, life was overwhelmingly microbial, and microbial metabolisms transformed the chemistry of oceans, rocks, atmosphere, and climate.

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Ecosystem Ecology

Water, Energy, and Ecosystem Dynamics

Ecosystems are physical and biological systems in which solar energy, water, and matter move together. Their dynamics emerge from the coupling of radiation, climate, soils, vegetation, microbial activity, and hydrologic flow.

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Biogeochemistry

Carbon Balances and Inputs from Terrestrial and Pelagic Sources

Photosynthesis is the main biological pathway by which inorganic carbon enters ecosystems. Terrestrial plants and marine phytoplankton both fix carbon, but they do so under very different constraints on water, nutrients, light, and physical structure.

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Ecosystem Ecology

Decomposition and Ecosystem Carbon Budgets

Photosynthesis brings carbon into ecosystems, but decomposition determines how long that carbon remains. Ecosystem carbon budgets depend on the balance between production, respiration, recycling, stabilization, export, and burial.

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Volume 3

2023

Issue 1

Summer 2022

Cover Feature

Microbial Adaptation, Genomes, and Environmental Change

Microbial ecology increasingly depends on connecting hidden genetic diversity to ecological function. This issue focuses on two ways that microbial ecologists make that connection: by resolving fine-scale adaptation within a dominant soil bacterium, and by reconstructing genomes from uncultivated microbes directly from environmental DNA.

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In This Issue

Dispatches and related readings

Microbial Ecology

Reconstructing Microbial Life from Metagenomes

Metagenome-assembled genomes have transformed microbial ecology by linking uncultivated lineages to metabolic traits, biogeochemical processes, and specialized metabolite potential. Yet MAGs are not direct observations of organisms; they are reconstructed genomic hypotheses whose power depends on community complexity, sequencing depth, strain structure, and careful interpretation.

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Inside the Paper

Microbial Adaptation Along a Climate Gradient

Microbial communities respond quickly to environmental change, but those responses are often interpreted as ecological shifts in community composition. Our PNAS paper asked whether microbial responses to climate also reflect evolutionary processes, using field experiments with Curtobacterium across a Southern California climate gradient.

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Issue 2

Fall 2023

Cover Feature

Chemical Biogeography and the Evolution of Microbial Chemistry

Microbial specialized metabolites are often treated as molecules to discover, but they are also ecological traits shaped by evolutionary history and environmental context. This issue focuses on two linked questions: how microbial chemistry evolves, and how that chemistry is organized across natural communities.

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In This Issue

Dispatches and related readings

Chemical Ecology

Biosynthetic Gene Clusters and the Evolution of Microbial Chemistry

Bacterial specialized metabolites are often studied as sources of new natural products, but their evolutionary histories also reveal how microbes diversify. Biosynthetic gene clusters can move, persist, fragment, recombine, and diverge, making microbial chemistry a powerful lens for understanding adaptation, ecological interaction, and lineage differentiation.

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Inside the Paper

Chemical Biogeography in Marine Sediments

Biogeography asks why organisms occur where they do, but in microbial communities the answer may depend as much on chemistry as on environment. In reef-associated marine sediments, we asked whether specialized metabolites help structure microbial communities across fine spatial scales. Our ISME Journal paper linked microbial composition, biosynthetic potential, and metabolome variation in natural sediments; follow-up SMIRC work then extended this logic by capturing natural products directly from the environments where these chemical interactions occur.

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Volume 2

2021

Issue 1

Fall 2021

Cover Feature

Microbial Chemical Ecology and Natural Products

Microbial natural products are often studied as sources of new drugs, but they are also ecological traits that shape how microbes interact, persist, and adapt. This issue explores specialized metabolism from discovery to function, emphasizing how genomes, metabolites, environments, and evolutionary history can be integrated to understand microbial chemistry.

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In This Issue

Dispatches and related readings

Natural Products

Finding Natural Products in Genomes and Metabolomes

Natural product discovery has shifted from bioassay-guided isolation toward integrated genomic and metabolomic approaches. Genome mining reveals biosynthetic potential, mass spectrometry detects expressed molecules, and heterologous expression helps connect orphan biosynthetic gene clusters to their chemical products.

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Chemical Ecology

Redox Chemistry as Microbial Chemical Ecology

Extracellular electron transfer shows that microbial metabolites are not only antibiotics, signals, or toxins. Redox-active molecules such as phenazines, quinones, and flavins can move electrons beyond the cell, linking microbial physiology to minerals, biofilms, sediments, and community-scale metabolism.

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Natural Products

Marine Sediments as Natural Product Discovery Systems

Marine sediments contain highly diverse and spatially heterogeneous microbial communities. Their low-energy conditions, steep chemical gradients, dormancy strategies, and long-term survival pressures make them promising systems for studying specialized metabolites as ecological traits.

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Inside the Paper

Specialized Metabolism and Species Differentiation in Salinispora

Salinispora is a rare marine sediment bacterium and model system for natural product discovery. Comparative genomics across nine species showed that biosynthetic gene clusters and metabolite profiles are structured more strongly by vertical inheritance than by frequent horizontal transfer.

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Issue 2

Spring 2020

Cover Feature

Microbes to Ecosystem Function

Microbial ecology is increasingly moving from describing community patterns to explaining their functional consequences. This issue focuses on that transition: how microbial diversity, biogeography, traits, and activity shape ecosystem processes across soils, oceans, plants, and biogeochemical cycles.

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In This Issue

Dispatches and related readings

Ecosystem Ecology

From Microbial Diversity to Ecosystem Function

Microbial communities influence ecosystem processes through traits that govern resource use, environmental tolerance, and interactions with plants, soils, and climate. Linking composition to function requires moving beyond diversity patterns toward trait-based frameworks that connect microbes to ecosystem outcomes.

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Biogeography

Microbial Biogeography Below the Community Level

Microbial biogeography is moving beyond broad community patterns toward the distribution of strains, populations, genes, and functional traits. Fine-scale genetic resolution reveals how geography, environment, recombination, and symbiosis structure microbial diversity across global, regional, and microscale habitats.

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Ecosystem Ecology

Linking Microbial Structure to Function

Microbial ecology increasingly aims to connect who is present with what communities do. Trait-based physiology, resistance and resilience frameworks, metatranscriptomics, and relic-DNA-aware sampling help link microbial community structure to functional responses across environmental change.

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Biogeochemistry

Microbial Traits as Signals of Ocean Biogeochemistry

Microbial genomes can record adaptation to nutrient availability. In surface oceans, nutrient-related genes in Prochlorococcus and Synechococcus provide trait-based signals that improve predictions of carbon, nitrogen, phosphorus, and iron cycling across biogeochemical regions.

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Volume 1

2019

Issue 1

Fall 2019

Cover Feature

Microdiversity and Fine-Scale Genetic Structure

Microbial diversity is often described through broad taxonomic units, but much of the ecology and evolution of microbes unfolds at a finer scale. Within what appears to be a single microbial “type” lies extensive microdiversity: closely related lineages that differ in genomic composition, ecological preference, functional traits, and evolutionary history. This issue highlights why resolving that fine-scale genetic structure is essential for understanding microbial biogeography.

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In This Issue

Dispatches and related readings

Biogeography

The Processes That Structure Microbial Diversity

Microbial diversity varies across environments, habitats, and spatial scales. Biogeography provides a framework for interpreting these patterns by linking community composition to selection, drift, dispersal, and diversification.

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Microbial Evolution

Microscale Habitats and the Early Stages of Bacterial Speciation

Closely related Vibrio populations can diverge across marine particle habitats despite sharing nearly identical marker genes. Genomic, ecological, and behavioral evidence suggests that particle association, dispersal, and habitat-specific recombination can structure early bacterial diversification.

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Microbial Ecology

Trait Variability and Niche Partitioning in Prochlorococcus

Nitrogen assimilation in Prochlorococcus reveals how microbial traits can diversify within closely related lineages. What appears at first to be a simple pattern of gene gain may instead reflect vertical inheritance, gene loss, homologous recombination, and ecological differentiation across ocean gradients.

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Microbial Ecology

Molecular Units Are Not Biological Units

Microbial ecology often treats OTUs, ASVs, genomes, strains, populations, and species as interchangeable units of diversity. They are not. Each molecular unit resolves a different scale of biological variation, and ecological inference depends on matching that scale to the traits, populations, and evolutionary processes being studied.

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Issue 2

Winter 2019

Cover Feature

Genes, Genomes, and the Scale of Microbial Evolution

Microbial evolution is often presented as rapid, flexible, and gene-centered, but the processes shaping microbial genomes are more constrained and context-dependent than that framing suggests. This issue examines how evolutionary change unfolds across microbiomes, pangenomes, mobile genetic elements, cultures, and reconstructed genomes.

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In This Issue

Dispatches and related readings

Microbial Evolution

Evolutionary Processes in Microbiomes

Microbiomes are often studied as ecological communities, but their composition also reflects ongoing evolutionary change. Selection, mutation, recombination, clonal interference, and cryptic genetic variation can reshape microbial traits within communities, making ecology and evolution difficult to separate.

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Microbial Evolution

Why Do Bacteria Have Pangenomes?

Bacterial genomes contain both conserved genes shared across related strains and flexible genes that vary among them. This pangenome structure raises a central evolutionary question: are flexible genes mostly neutral, deleterious, adaptive, or context-dependent?

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Microbial Evolution

Horizontal Gene Transfer and the Boundaries of Microbial Evolution

Horizontal gene transfer can move genes across distant lineages, rapidly altering microbial traits and ecological potential. Yet HGT also complicates microbial evolution: it can blur lineage boundaries, create mosaic genomes, and obscure the difference between recent adaptive transfer and ancient evolutionary history.

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Microbial Diversity

Cultures, MAGs, and the Problem of Representation

Culture collections, marker-gene surveys, and metagenome-assembled genomes each reveal different dimensions of microbial diversity. The central question is not which method is “right,” but whether the biological unit being inferred is representative of the diversity, traits, and evolutionary structure present in the environment.

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