Knowing When to Draw the Line: Designing More Informative Ecological Experiments

Linear regression and analysis of variance (ANOVA) are two of the most widely used statistical techniques in ecology. Regression quantitatively describes the relationship between a response variable and one or more continuous independent variables, while ANOVA determines whether a response variable differs among discrete values of the independent variable(s). Designing experiments with discrete factors is straightforward because ANOVA is the only option, but what is the best way to design experiments involving continuous factors? Should ecologists prefer experiments with few treatments and many replicates analyzed with ANOVA, or experiments with many treatments and few replicates per treatment analyzed with regression? We recommend that ecologists choose regression, especially replicated regression, over ANOVA when dealing with continuous factors for two reasons: (1) regression is generally a more powerful approach than ANOVA and (2) regression provides quantitative output that can be incorporated into ecological models more effectively than ANOVA output

Complete Genome Sequence of Cyanobacterial Siphovirus KBS2A

Abstract We present the genome of a cyanosiphovirus (KBS2A) that infects a marine Synechococcus sp. (strain WH7803). Unique to this genome, relative to other sequenced cyanosiphoviruses, is the absence of elements associated with integration into the host chromosome, suggesting this virus may not be able to establish a lysogenic relationship. Go to: GENOME ANNOUNCEMENT As obligate parasites, viruses can regulate their host population dynamics but also influence the structure and productivity of microbial communities (1, 2). Synechococcus species are an abundant and ecologically important group of Cyanobacteria found in freshwater and marine ecosystems worldwide. Virus-cyanobacterium interactions may have important implications for global biogeochemical cycles. The most commonly isolated cyanophages are myoviruses and podoviruses (3, 4). Siphoviruses are a third group of viruses that infect cyanobacteria, but they have received less attention (5). The genomes of 5 cyanosiphoviruses have recently become available: that of P-SS2, a siphovirus infecting Prochlorococcus (MIT9313) (6), followed by the cyanosiphoviruses S-CBS1, S-CBS2, S-CBS3, and S-CBS4, isolated from the Chesapeake Bay Estuary, all infecting Synechococcus populations (5). Here, we present the complete genome of cyanosiphophage (KBS2A, originally named KBS-S-2A), a virus that infects Synechococcus sp. strain WH7803. The virus was isolated by plaque assay from the Chesapeake Bay by plating on Synechococcus sp. WH7803. Purified virus DNA was submitted to the Broad Institute as part of the Marine Phage Sequencing Project, where it was sequenced to ~30-fold coverage using 454 pyrosequencing. Translated open reading frames (ORFs) were compared with known protein sequences using the BLASTp program. ORF annotation was aided by the use of PSI-BLAST, HHpred, gene size, and domain conservation. The genome size of KBS2A is 40,658 bp. In total, 64 ORFs have been predicted in this genome; of these, 43 have homologues in databases, and among them, 33 have been assigned to a putative function. For most (88%) predicted ORFs with homologues, homology has been found with the other cyanosiphovirus genomes. We compared the genomic arrangements of the 6 sequenced cyanosiphoviruses using dot plot and global gene homology and found no common genomic organization, suggesting strong mosaicism in the cyanosiphoviruses. In cyanophages, cyanobacterium-related proteins can be found and are often associated with photosynthesis and transcriptional regulation (6). In previously sequenced cyanosiphovirus genomes (5, 6), numerous viral genes (6 to 40 per genome) possess homology with host genes. In the case of the KBS2A genome, only 3 ORFs (coding for RNA polymerase sigma factor RpoD, HNH endonuclease, and a putative DNA polymerase) show such homology, implying less exchange (and potentially interaction) with the host genome. The first annotated cyanosiphovirus genome (that of P-SS2) showed the presence of genes identified as encoding an integrase and excisionase, which are enzymes that allow for phage integration into the host’s genome (6). Moreover, the annotation of cyanosiphoviruses S-CBS1 and S-CBS3 led to the discovery of a prophage-like structure in two sequenced Synechococcus elongatus strains (5). In phage genomes, tRNA genes serve as indicators of potential phage integration by site-specific recombination (7, 8), although recent models have offered alternative suggestions for the role of these genes (9). Sequences of this nature can, however, be found in the P-SS2 and S-CBS4 genomes. No such features (tRNAs, integrases, etc.) were found in the genome of KBS2A, suggesting that this siphovirus might be an exclusively lytic phage rather than a temperate phage. Nucleotide sequence accession number. The complete sequence of the Synechococcus phage KBS2A genome can be accessed under the GenBank accession no. HQ634187. doi: 10.1128/genomeA.00472-1

Denitrification by sulfur-oxidizing bacteria in a eutrophic lake

Understanding the mechanistic controls of microbial denitrification is of central importance to both environmental microbiology and ecosystem ecology. Loss of nitrate (NO3 −) is often attributed to carbon-driven (heterotrophic) denitrification. However, denitrification can also be coupled to sulfur (S) oxidation by chemolithoautotrophic bacteria. In the present study, we used an in situ stable isotope (15NO3 −) tracer addition in combination with molecular approaches to understand the contribution of sulfur-oxidizing bacteria to the reduction of NO3 − in a eutrophic lake. Samples were incubated across a total dissolved sulfide (H2S) gradient (2 to 95 μM) between the lower epilimnion and the upper hypolimnion. Denitrification rates were low at the top of the chemocline (4.5 m) but increased in the deeper waters (5.0 and 5.5 m), where H2S was abundant. Concomitant with increased denitrification at depths with high sulfide was the production of sulfate (SO4 2−), suggesting that the added NO3 − was used to oxidize H2S to SO4 2−. Alternative nitrate removal pathways, including dissimilatory nitrate reduction to ammonium (DNRA) and anaerobic ammonium oxidation (anammox), did not systematically change with depth and accounted for 1 to 15% of the overall nitrate loss. Quantitative PCR revealed that bacteria of the Sulfurimonas genus that are known denitrifiers increased in abundance in response to NO3 − addition in the treatments with higher H2S. Stoichiometric estimates suggest that H2S oxidation accounted for more than half of the denitrification at the depth with the highest sulfide concentration. The present study provides evidence that microbial coupling of S and nitrogen (N) cycling is likely to be important in eutrophic freshwater ecosystems

Hypersaline lakes harbor more active bacterial communities

ABSTRACT Extremophiles employ a diverse array of resistance strategies to thrive under harsh 18 environmental conditions but maintaining these adaptations comes at an energetic cost. If energy reserves to drop too low, extremophiles may enter a dormant state of reduced 20 metabolic activity to survive. Dormancy is frequently offered as a plausible explanation for the persistence of bacteria under suboptimal environmental conditions with the 22 prevalence of this mechanism only expected to rise as stressful conditions intensify. We estimated dormancy in ten hypersaline and freshwater lakes across the Western United 24 States. To our surprise, we found that extreme environmental conditions did not induce higher levels of bacterial dormancy. Based on our approach using rRNA:rDNA gene 26 ratios to estimate activity, halophilic and halotolerant bacteria were classified as inactive at a similar percentage as freshwater bacteria, and the proportion of the community 28 exhibiting dormancy was considerably lower (16%) in hypersaline than freshwater lakes across a range of cutoffs estimating activity. Of the multiple chemical characteristics we 30 evaluated, salinity and, to a lesser extent, total phosphorus concentrations influenced activity. But instead of dormancy being more common as stressful conditions intensified, 32 the percentage of the community residing in an inactive state decreased with increasing salinity in freshwater and hypersaline lakes, suggesting that salinity acts as a strong 34 environmental filter selecting for bacteria that persist and thrive under saltier conditions. Within the compositionally distinct and less diverse hypersaline communities, abundant 36 taxa were disproportionately active and localized in families Microbacteriacea

Ecological networks of dissolved organic matter and microorganisms under global change

Microbes regulate the composition and turnover of organic matter. Here we developed a framework called Energy-Diversity-Trait integrative Analysis to quantify how dissolved organic matter and microbes interact along global change drivers of temperature and nutrient enrichment. Negative and positive interactions suggest decomposition and production processes of organic matter, respectively. We applied this framework to manipulative field experiments on mountainsides in subarctic and subtropical climates. In both climates, negative interactions of bipartite networks were more specialized than positive interactions, showing fewer interactions between chemical molecules and bacterial taxa. Nutrient enrichment promoted specialization of positive interactions, but decreased specialization of negative interactions, indicating that organic matter was more vulnerable to decomposition by a greater range of bacteria, particularly at warmer temperatures in the subtropical climate. These two global change drivers influenced specialization of negative interactions most strongly via molecular traits, while molecular traits and bacterial diversity similarly affected specialization of positive interactions. Microbes are intimately linked with the fate of organic matter. Here the authors develop an ecological network framework and show how microbes and dissolved organic matter interact along global change drivers of temperature and nutrient enrichment via manipulative field experiments on mountains.Peer reviewe

Integrating microbial ecology into ecosystem models: challenges and priorities

Microbial communities can potentially mediate feedbacks between global change and ecosystem function, owing to their sensitivity to environmental change and their control over critical biogeochemical processes. Numerous ecosystem models have been developed to predict global change effects, but most do not consider microbial mechanisms in detail. In this idea paper, we examine the extent to which incorporation of microbial ecology into ecosystem models improves predictions of carbon (C) dynamics under warming, changes in precipitation regime, and anthropogenic nitrogen (N) enrichment. We focus on three cases in which this approach might be especially valuable: temporal dynamics in microbial responses to environmental change, variation in ecological function within microbial communities, and N effects on microbial activity. Four microbially-based models have addressed these scenarios. In each case, predictions of the microbial-based models differ—sometimes substantially—from comparable conventional models. However, validation and parameterization of model performance is challenging. We recommend that the development of microbial-based models must occur in conjunction with the development of theoretical frameworks that predict the temporal responses of microbial communities, the phylogenetic distribution of microbial functions, and the response of microbes to N enrichment

The under-ice microbiome of seasonally frozen lakes

Compared to the well-studied open water of the “growing” season, under-ice conditions in lakes are characterized by low and rather constant temperature, slow water movements, limited light availability, and reduced exchange with the surrounding landscape. These conditions interact with ice-cover duration to shape microbial processes in temperate lakes and ultimately influence the phenology of community and ecosystem processes. We review the current knowledge on microorganisms in seasonally frozen lakes. Specifically, we highlight how under-ice conditions alter lake physics and the ways that this can affect the distribution and metabolism of auto- and heterotrophic microorganisms. We identify functional traits that we hypothesize are important for understanding under-ice dynamics and discuss how these traits influence species interactions. As ice coverage duration has already been seen to reduce as air temperatures have warmed, the dynamics of the under-ice microbiome are important for understanding and predicting the dynamics and functioning of seasonally frozen lakes in the near future