Biology subjects

Lennon, J. T.

Publications and source records attributed to Lennon, J. T..

7 recordsLinked to original sources

bioRxiv2018

Microbial dormancy improves predictability of soil respiration at the seasonal time scale

Climate change is accelerating global soil respiration, which could in turn accelerate climate change. The biological mechanisms through which soil carbon (C) responds to climate are not well understood, limiting our ability to predict future global soil respiration rates. As part of a climate manipulation experiment, we tested whether differences in soil heterotrophic respiration driven by season or climate treatment (RH) are linked to 1) relative abundances of microbes in active and dormant metabolic states, 2) net changes in microbial biomass and/or 3) changes in the relative abundances of microbial groups with different C-use strategies. We used a flow-cytometric single-cell metabolic assay to quantify the abundance of active and dormant microbes, and the phospholipid fatty acid (PLFA) method to determine microbial biomass and ratios of fungi:bacteria and Gram-positive:Gram-negative bacteria. RH did not respond to climate treatments but was greater in the warm and dry summer than in the cool and less-dry fall. These dynamics were better explained when microbial data were taken into account compared to when only physical data (temperature and moisture) were used. Overall, our results suggest that RH responses to temperature are stronger when soil contains more active microbes, and that seasonal patterns of RH can be better explained by shifts in microbial activity than by shifts in the relative abundances of fungi and Gram-positive and Gram-negative bacteria. These findings contribute to our understanding of how and under which conditions microbes influence soil C responses to climate.

microbiology↗

bioRxiv2018

Trait-based approach to bacterial growth efficiency

AO_SCPLOWBSTRACTC_SCPLOWBacterial growth efficiency (BGE) is the proportion of assimilated carbon that is converted into biomass and reflects the balance between growth and energetic demands. Often measured as an aggregate property of the community, BGE is highly variable within and across ecosystems. To understand this variation, we first identified how species identity and resource type affect BGE using 20 bacterial isolates belonging to the phylum Proteobacteria that were enriched from north temperate lakes. Using a trait-based approach that incorporated genomic and phenotypic information, we characterized the metabolism of each isolate and tested for predicted trade-offs between growth rate and efficiency. A substantial amount of variation in BGE could be explained at both broad (i.e., order, 20 %) and fine (i.e., strain, 58 %) taxonomic levels. While resource type was a relatively weak predictor across species, it explained > 60 % of the variation in BGE within a given species. Furthermore, a metabolic trade-off (between maximum growth rate and efficiency) and genomic features revealed that BGE is a predictable metabolic feature. Our study suggests that genomic and phylogenetic information may help predict aggregate microbial community functions like BGE and the fate of carbon in ecosystems. OO_SCPLOWRIGINALITYC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWANDC_SCPLOW SO_SCPLOWIGNIFICANCEC_SCPLOWBacterial growth efficiency (BGE) is an important yet notoriously variable measure of metabolism that has proven difficult to predict. To better understand how assimilated carbon is allocated, we explored growth efficiency across a collection of bacteria strains using a trait-based approach. Specifically, we measured respiration and biomass formation rates for populations grown in minimal media containing one of three carbon resources. In addition, we collected a suite of physiological traits to describe each strain, and we sequenced the genome of each organism. Our results suggest that species identity and resource type may contribute to growth efficiency when measured as an aggregate property of a natural community. In addition, we identified genomic pathways that are associated with elevated BGE. The findings have implications for integrating microbial metabolism from the cellular to ecosystem scale.

microbiology↗

bioRxiv2018

Diversity and composition of cave methanotrophic communities

Methane oxidizing microorganisms (methanotrophs) are ubiquitous in the environment and represent a major sink for the greenhouse gas methane (CH4). Recent studies have demonstrated that methanotrophs are abundant and contribute to CH4 dynamics in caves. However, very little is known about what controls the distribution and abundance of methanotrophs in subterranean ecosystems. Here, we report a survey of soils collected from > 20 caves in North America to elucidate the factors shaping cave methanotroph communities. Using 16S rRNA sequencing, we recovered methanotrophs from nearly all (98 %) of the samples, including cave sites where CH4 concentrations were at or below detection limits ([≤] 0.3 ppmv). We identified a core methanotroph community among caves that was comprised of high-affinity methanotrophs. Although associated with local-scale mineralogy, methanotroph composition did not systematically vary between the entrances and interior of caves, where CH4 concentrations varied. We also observed that methanotrophs are able to disperse readily between cave systems showing these organisms have low barriers to dispersal. Last, the relative abundance of methanotrophs was positively correlated with cave-air CH4 concentrations suggesting that these microorganisms contribute to CH4 flux in subterranean ecosystems. IMPORTANCERecent observations have shown that the atmospheric greenhouse gas methane (CH4) is consumed by microorganisms (methanotrophs) in caves at rates comparable to CH4 oxidation in surface soils. Caves are abundant in karst landscapes that comprise 14 % of Earths land surface area, and therefore may represent a potentially important, but overlooked CH4 sink. We sampled cave soils to gain a better understand the community composition and structure of cave methanotrophs. Our results show that the members of the USC-{gamma} clade are dominant in cave communities and can easily disperse through the environment, that methanotroph relative abundance was correlated with local scale mineralogy of soils, and that the relative abundance of methanotrophs was positively correlated with CH4 concentrations in cave air.

microbiology↗

bioRxiv2018

Resource diversity structures aquatic bacterial communities

Microbial diversity is strongly affected by the bottom-up effects of resource availability. However, because resource pools often exist as heterogeneous mixtures of distinct molecules, resource heterogeneity may also affect community diversity. To test this hypothesis, we surveyed bacterial communities in lakes that varied in resource concentration. In addition, we characterized resource heterogeneity in these lakes using an ecosystem metabolomics approach. Overall, resource concentration and resource heterogeneity affected bacterial resource-diversity relationships. We found strong relationships between bacterial alpha-diversity (richness and evenness) and resource concentration and richness, but richness and evenness responded in different ways. Likewise, we found associations between the composition of the bacterial community and both resource concentration and composition, but the relationship with resource composition was stronger. Last, in the surveyed communities the presence of resource generalists may have reduced the effect of resource heterogeneity on community composition. These results have implications for understanding the interactions between bacteria and organic matter and suggest that changes in organic matter composition may alter the structure and function of bacterial communities.

microbiology↗

bioRxiv2017

Nutrient stoichiometry shapes microbial coevolution

Coevolution is a force contributing to the generation and maintenance of biodiversity. It is influenced by environmental conditions including the scarcity of essential resources, which can drive the evolution of defense and virulence traits. We conducted a long-term chemostat experiment where the marine cyanobacterium Synechococcus was challenged with a lytic phage under nitrogen (N) or phosphorus (P) limitation. This manipulation of nutrient stoichiometry altered the stability of host-parasite interactions and the underlying mode of coevolution. By assessing infectivity with >18,000 pairwise challenges, we documented directional selection for increased phage resistance, consistent with arms-race dynamics while phage infectivity fluctuated through time, as expected when coevolution is driven by negative frequency-dependent selection. The resulting infection networks were 50 % less modular under N-versus P-limitation reflecting host-range contraction and asymmetric coevolutionary trajectories. Nutrient stoichiometry affects eco-evolutionary feedbacks in ways that may alter the dynamics and functioning of environmental and host-associated microbial communities.

microbiology↗

bioRxiv2017

Evolution with a seed bank: the population genetic consequences of microbial dormancy

Dormancy is a bet-hedging strategy that allows organisms to persist through conditions that are sub-optimal for growth and reproduction by entering a reversible state of reduced metabolic activity. Dormancy allows a population to maintain a reservoir of genetic and phenotypic diversity (i.e., a seed bank) that can contribute to the long-term survival of a population. This strategy can be potentially adaptive and has long been of interest to ecologists and evolutionary biologists. However, comparatively little is known about how dormancy influences the fundamental evolutionary forces of genetic drift, mutation, selection, recombination, and gene flow. Here, we investigate how seed banks affect the processes underpinning evolution by reviewing existing theory, implementing novel simulations, and determining how and when dormancy can influence evolution as a population genetic process. We extend our analysis to examine how seed banks can alter macroevolutionary processes, including rates of speciation and extinction. Through the lens of population genetic theory, we can understand the extent that seed banks influence microbial evolutionary dynamics.

microbiology↗

bioRxiv2017

Relic DNA contributes minimally to estimates of microbial diversity

Extracellular or \"relic\" DNA is one of the largest pools of nucleic acids in the mbiosphere 1,2. Relic DNA can influence a number of important ecological and evolutionary processes, but it may also bias estimates of microbial abundance and diversity, which has implications for understanding environmental, engineered, and host-associated ecosystems. We developed models capturing the fundamental processes that regulate the size and composition of the relic DNA pools to identify scenarios leading to biased estimates of biodiversity. Our models predict that bias increases with relic DNA pool size, but only when the species abundance distributions (SAD) of relic and intact DNA are distinct from one another. We evaluated our model predictions by quantifying relic DNA and assessing its contribution to bacterial diversity using 16S rRNA gene sequences collected from different ecosystem types, including soil, sediment, water, and the mammalian gut. On average, relic DNA made up 33 % of the total bacterial DNA pool, but exceeded 80 % in some samples. Despite its abundance, relic DNA had no effect on estimates of taxonomic and phylogenetic diversity, even in ecosystems where processes such as the physical protection of relic DNA are common and predicted by our models to generate bias. Rather, our findings are consistent with the expectation that relic DNA sequences degrade in proportion to their abundance and therefore may contribute minimally to estimates of microbial diversity.

microbiology↗