Jennifer B.H. Martiny

University of California, Irvine | UCI · Department of Ecology and Evolutionary Biology

Significance Increasing evidence suggests that evolutionary processes frequently shape ecological patterns; however, most microbiome studies thus far have focused on only the ecological responses of these communities. By using parallel field experiments and focusing in on a model soil bacterium, we showed that bacterial “species” are differentially...

Course-based undergraduate research experiences (CUREs) are an effective way to introduce students to contemporary scientific research. Research experiences have been shown to promote critical thinking, improve understanding and proper use of the scientific method, and help students learn practical skills including writing and oral communication. W...

The high diversity of soil bacteria is attributed to the spatial complexity of soil systems, where habitat heterogeneity promotes niche partitioning among bacterial taxa. This premise remains challenging to test, however, as it requires quantifying the traits of closely‐related soil bacteria and relating these traits to bacterial abundances and geo...

Microbial decomposers mediate the return of CO2 to the atmosphere by producing extracellular enzymes to degrade complex plant polymers, making plant carbon available for metabolism. Determining if and how these decomposer communities are constrained in their ability to degrade plant litter is necessary for predicting how carbon cycling will be affe...

Plant and animal diversity generally increases with increasing environmental heterogeneity. Here, we test whether this relationship also holds for bacterial communities in soil. Specifically, we investigate whether invasive annual grasslands have reduced soil heterogeneity and, thereby, decreased bacterial alpha- and beta-diversity. Soils were samp...

Much genetic diversity within a bacterial community is likely obscured by microdiversity within operational taxonomic units (OTUs) defined by 16S rRNA gene sequences. However, it is unclear how variation within this microdiversity influences ecologically relevant traits. Here, we employ a multifaceted approach to investigate microdiversity within t...

Dispersal is central to the evolution and maintenance of microbial diversity. Quantifying microbial dispersal and its role in shaping communities remains a challenge, however. Here, we manipulated a bacterial community’s dispersal rate in a grassland ecosystem and test whether this altered diversity and composition. We constructed bags of two nylon...

Environmental change will influence the ecosystem processes regulated by microbial communities, including leaf litter decomposition. To assess how microbial communities and their functioning might respond to increases in temperature, we quantified the distribution of traits related to carbon substrate utilization and temperature sensitivity in leaf...

Decomposition rates for each bacterial isolate. Cumulative CO2 production rates for each bacterial isolate across three temperature treatments. N = 3 for each box. (EPS)

Biolog EcoPlate and decomposition data. Raw microcosm and CO2 production data for all isolates across three temperature treatments. (XLSX)

Substrate use richness for each isolate. The number of substrates utilized by the bacterial isolates across the three temperatures. (EPS)

Substrate use richness at each temperature. Substrate use richness for all bacterial isolates for each temperature treatment. N = 15 for each temperature treatment. (EPS)

Principle Coordinates Analysis (PCA) of functional and response traits. PCA ordination based on Euclidian distances of normalized functional and response traits. All functional traits are based on the mean value across all temperatures and, when applicable, EcoPlate substrates. The color of the symbols represent the phyla: Proteobacteria (green), A...

Viruses of marine cyanobacteria frequently contain auxiliary metabolic genes (AMGs) that augment host metabolism during infection, but little is known about their adaptive significance. We analyzed the distribution and genomic context of 33 AMGs across 60 cyanomyovirus genomes. Similarity in AMG content among cyanomyoviruses was only weakly correla...

Assigning ecological roles to bacterial taxa remains imperative to understanding how microbial communities will respond to changing environmental conditions. Here we analyze the genus Curtobacterium, as it was found to be the most abundant taxon in a leaf litter community in southern California. Traditional characterization of this taxon predominan...

Terrestrial ecosystem models assume that microbial communities respond instantaneously, or are immediately resilient, to environmental change. Here we tested this assumption by quantifying the resilience of a leaf litter community to changes in precipitation or nitrogen availability. By manipulating composition within a global change experiment, we...

Understanding the structure and origin of natural bacteriophage genomic diversity is important in elucidating how bacteriophages influence the mortality rates and composition of their host communities. Here we examine the genetic structure and genomic diversification of naturally occurring bacteriophages by analyzing the full genomic sequences of o...

Stochastic processes can play an important role in microbial community assembly. Dispersal limitation is one process that can increase stochasticity and obscure relationships between environmental variables and microbial community composition, but the relationship between dispersal, selection and stochasticity has not been described in a comprehens...

Following the success of the inaugural games, the Microbial Olympics return with a new series of events and microbial competitors. The games may have moved to a new hosting venue, but the dedication to training, fitness, competition (and yes, education and humour) lives on.

Microorganisms drive much of the Earth's nitrogen (N) cycle, but we still lack a global overview of the abundance and composition of the microorganisms carrying out soil N processes. To address this gap, we characterized the biogeography of microbial N traits, defined as eight N-cycling pathways, using publically available soil metagenomes. The rel...

Dispersal is closely tied to the origin and maintenance of microbial diversity. With its focus on a narrow group of soil bacteria, recent work by Andam and colleagues on Streptomyces has provided perhaps the strongest support so far that some bacterial diversity in soils can be attributed to regional endemism (C. P. Andam et al., mBio 7:e02200-15,...

Despite the important role of phages in marine systems, little is understood about how their diversity is distributed in space. Biogeographic patterns of marine phages may be difficult to detect due to their vast genetic diversity, which may not be accurately represented by conserved marker genes. To investigate the spatial biogeographic structure...

Function in the tree of life How does the composition of microbial communities integrate functionally with the wider environment? Martiny et al. review how patterns of microbial species abundances in different environments and disease states can have strong evolutionary signals. Some environmental changes select the survival of organisms with conse...

Recent studies demonstrate that microorganisms are sensitive to environmental change, and that their community composition influences ecosystem functioning. However, it is unknown whether microbial composition interacts with the environment to affect the response of ecosystem processes to changing abiotic conditions. To investigate the potential fo...

Because microorganisms have different abilities to utilize nitrogen (N) through various assimilatory and dissimilatory pathways, microbial composition and diversity likely influences N cycling in an ecosystem. Terrestrial plant litter decomposition is often limited by N availability; however, little is known about the microorganisms involved in lit...

The high diversity of microbial communities hampers predictions about their responses to global change. Here we investigate the potential for using a phylogenetic, trait-based framework to capture the response of bacteria and fungi to global change manipulations. Replicated grassland plots were subjected to 3+ years of drought and nitrogen fertiliz...

Bacteria and fungi drive the decomposition of dead plant biomass (litter), an important step in the terrestrial carbon cycle. Here we investigate the sensitivity of litter microbial communities to simulated global change (drought and nitrogen addition) in a California annual grassland. Using 16S and 28S rDNA amplicon pyrosequencing, we quantify the...

Even if a microorganism can be found everywhere, it can also be dispersal limited. The extent of dispersal limitation influences the generation and maintenance of microbial diversity. Biogeographic patterns suggest that even free-living microbes are dispersal limited. Estimates of microbial dispersal rates are needed to understand the relative role...

Changes in nitrification rates due to climate change have the potential to influence soil nitrogen availability, water quality, and greenhouse gas emissions. However, the mechanisms through which temperature and precipitation affect nitrification and the nitrifying microbial community in the field are largely unknown. We examined the effects of war...

Fungi play a critical role in the degradation of organic matter. Because different combinations of fungi result in different rates of decomposition, determining how climate change will affect microbial composition and function is fundamental to predicting future environments. Fungal response to global change is patterned by genetic relatedness, res...

In many ecosystems, global changes are likely to profoundly affect microorganisms. In Southern California, changes in precipitation and nitrogen deposition may influence the composition and functional potential of microbial communities and their resulting ability to degrade plant material.To test whether such environmental changes impact the distri...

Salt marshes provide storm protection to shorelines, sequester carbon (C) and mitigate coastal eutrophication. These valuable coastal ecosystems are confronted with increasing nitrogen (N) inputs from anthropogenic sources such as agricultural runoff, wastewater, and atmospheric deposition. To inform predictions of salt marsh functioning and sustai...

Background/Question/Methods Future global changes are predicted to alter ecosystem processes such as leaf litter decomposition. Such environmental changes may affect functioning directly, through changes in abiotic conditions, and indirectly, through changes in microbial and plant communities. The importance of microbial composition for functioni...

Background/Question/Methods Microbes such as Bacteria and Fungi play a critical role in the degradation of organic matter. Different combinations of microbial taxa result in different rates of decomposition, so predicting how climate change will affect microbial composition and function is fundamental to understanding future environments. However...

To explore the potential linkage between distribution of marine bacterioplankton groups, environmental conditions, and water mass, we investigated the factors determining the abundance of bacterial taxa across the hydrographically complex Subtropical Convergence Zone in the Sargasso Sea. Based on information from 16S rRNA gene clone libraries from...

Microbial biogeography examines the distribution of microorganisms over space and time, shedding light on the relative importance of the ecological and evolutionary processes that lead to those distributions. This “map” of microbial diversity also aids in predicting the response of microbes, and the ecosystem processes they mediate, to changing env...

Typically defined as unicellular life forms only observed with a microscope, microorganisms span all three domains of life, including bacteria, archaea, viruses, and eukaryotes. This article asks three fundamental questions about microbial diversity: How do we measure it? How much is there? What is its role in ecosystems? To address these questions...

Recent advances in sequencing technologies generate new predictions and hypotheses about the functional roles of environmental microorganisms. Yet, until we can test these predictions at a scale that matches our ability to generate them, most of them will remain as hypotheses. Function-based mining of metagenomic libraries can provide direct linkag...

Factors controlling the spatial distribution of bacterial diversity have been intensely studied, whereas less is known about temporal changes. To address this, we tested whether the mechanisms that underlie bacterial temporal beta-diversity vary across different scales in three marine microbial communities. While seasonal turnover was detected, at...

The potential for antagonistic coevolution between marine viruses and their (primarily bacterial) hosts is well documented, but our understanding of the consequences of this rapid evolution is in its infancy. Acquisition of resistance against co-occurring viruses and the subsequent evolution of virus host range in response have implications for bac...

Marine ecosystems contain an immense diversity of phages, many of which infect the cyanobacteria responsible for a portion of oceanic primary productivity. To add to the growing body of research on the dynamics and diversity of these cyanophages, we measured cyanophage abundance, diversity, and community composition monthly for 15 mo at 3 coastal l...

To test whether within-species and among-species patterns of abundance and latitudinal range in marine bacteria resemble those found for macro-organisms, and whether these patterns differ along latitudinal clines. Global pelagic marine environments. Taxon-specific sequence abundance and location were retrieved from the open-access V6-rRNA pyrotag s...

Rates of ecosystem processes such as decomposition are likely to change as a result of human impacts on the environment. In southern California, climate change and nitrogen (N) deposition in particular may alter biological communities and ecosystem processes. These drivers may affect decomposition directly, through changes in abiotic conditions, an...

Microbial communities are at the heart of all ecosystems, and yet microbial community behavior in disturbed environments remains difficult to measure and predict. Understanding the drivers of microbial community stability, including resistance (insensitivity to disturbance) and resilience (the rate of recovery after disturbance) is important for pr...

Although microorganisms largely drive many ecosystem processes, the relationship between microbial composition and their functioning remains unclear. To tease apart the effects of composition and the environment directly, microbial composition must be manipulated and maintained, ideally in a natural ecosystem. In this study, we aimed to test whethe...

Biogeographic patterns have been demonstrated for a wide range of microorganisms. Nevertheless, the biogeography of marine viruses has been slower to emerge. Here we investigate biogeographic patterns of marine cyanophages that infect Synechococcus sp. WH7803 across multiple spatial and temporal scales. We compared cyanophage myoviral communities f...

Recently, microbiologists have established the existence of biogeographic patterns among a wide range of microorganisms. The focus of the field is now shifting to identifying the mechanisms that shape these patterns. Here, we propose that four processes - selection, drift, dispersal and mutation - create and maintain microbial biogeographic pattern...

Methane (CH(4)) flux from ecosystems is driven by C(1)-cycling microorganisms - the methanogens and the methylotrophs. Little is understood about what regulates these communities, complicating predictions about how global change drivers such as nitrogen enrichment will affect methane cycling. Using a nitrogen addition gradient experiment in three S...

Marine viruses impose a heavy mortality on their host bacteria, whereas at the same time the degree of viral resistance in marine bacteria appears to be high. Antagonistic coevolution--the reciprocal evolutionary change of interacting species--might reconcile these observations, if it leads to rapid and dynamic levels of viral resistance. Here we d...

Marine viruses have only relatively recently come to the attention of molecular biologists, and the extraordinary diversity of potential host organisms suggests a new wealth of genetic and structural forms. A promising technology for characterizing and describing the viruses structurally is atomic force microscopy (AFM). We provide examples here of...

Pink-pigmented facultative methylotrophic bacteria (PPFMs) are associated with the roots, leaves and seeds of most terrestrial plants and utilize volatile C(1) compounds such as methanol generated by growing plants during cell division. PPFMs have been well studied in agricultural systems due to their importance in crop seed germination, yield, pat...

After removing invasive plants, whether by herbicides or other means, typical restoration design focuses on rebuilding native plant communities while disregarding soil microbial communities. However, microbial–plant interactions are known to influence the relative success of native versus invasive plants. Therefore, the abundance and composition of...