Leucine incorporation by aerobic anoxygenic phototrophic bacteria in the Delaware estuary

Ecology of aerobic anoxygenic phototrophs on a fine-scale taxonomic resolution in Adriatic Sea unravelled by unsupervised neural network

BACKGROUND

Aerobic anoxygenic phototrophs are metabolically highly active, diverse and widespread polyphyletic members of bacterioplankton whose photoheterotrophic capabilities shifted the paradigm about simplicity of the microbial food chain. Despite their considerable contribution to the transformation of organic matter in marine environments, relatively little is still known about their community structure and ecology at fine-scale taxonomic resolution. Up to date, there is no comprehensive (i.e. qualitative and quantitative) analysis of their community composition in the Adriatic Sea.

RESULTS

Analysis was based on pufM gene metabarcoding and quantitative FISH-IR approach with the use of artificial neural network. Significant seasonality was observed with regards to absolute abundances (maximum average abundances in spring 2.136 ± 0.081 × 104 cells mL-1, minimum in summer 0.86 × 104 cells mL-1), FISH-IR groups (Roseobacter clade prevalent in autumn, other Alpha- and Gammaproteobacteria in summer) and pufM sequencing data agglomerated at genus-level. FISH-IR results revealed heterogeneity with the highest average relative contribution of AAPs assigned to Roseobacter clade (37.66%), followed by Gammaproteobacteria (35.25%) and general Alphaproteobacteria (31.15%). Community composition obtained via pufM sequencing was dominated by Gammaproteobacteria clade NOR5/OM60, specifically genus Luminiphilus, with numerous rare genera present in relative abundances below 1%. The use of artificial neural network connected this community to biotic (heterotrophic bacteria, HNA and LNA bacteria, Synechococcus, Prochlorococcus, picoeukaryotes, heterotrophic nanoflagellates, bacterial production) and abiotic environmental factors (temperature, salinity, chlorophyll a and nitrate, nitrite, ammonia, total nitrogen, silicate, and orthophosphate concentration). A type of neural network, neural gas analysis at order-, genus- and ASV-level, resulted in five distinct best matching units (representing particular environments) and revealed that high diversity was generally independent of temperature, salinity, and trophic status of the environment, indicating a potentially dissimilar behaviour of aerobic anoxygenic phototrophs compared to the general bacterioplankton.

CONCLUSION

This research represents the first comprehensive analysis of aerobic anoxygenic phototrophs in the Adriatic Sea on a trophic gradient during a year-round period. This study is also one of the first reports of their genus-level ecology linked to biotic and abiotic environmental factors revealed by unsupervised neural network algorithm, paving the way for further research of substantial contribution of this important bacterial functional group to marine ecosystems.

Aerobic Anoxygenic Phototrophic Bacteria in the Marine Environments Revealed by Raman/Fluorescence-Guided Single-Cell Sorting and Targeted Metagenomics

Aerobic anoxygenic phototrophic bacteria (AAPB) contribute profoundly to the global carbon cycle. However, most AAPB in marine environments are uncultured and at low abundance, hampering the recognition of their functions and molecular mechanisms. In this study, we developed a new culture-independent method to identify and sort AAPB using single-cell Raman/fluorescence spectroscopy. Characteristic Raman and fluorescent bands specific to bacteriochlorophyll a (Bchl a) in AAPB were determined by comparing multiple known AAPB with non-AAPB isolates. Using these spectroscopic biomarkers, AAPB in coastal seawater, pelagic seawater, and hydrothermal sediment samples were screened, sorted, and sequenced. 16S rRNA gene analysis and functional gene annotations of sorted cells revealed novel AAPB members and functional genes, including one species belonging to the genus Sphingomonas, two genera affiliated to classes Betaproteobacteria and Gammaproteobacteria, and function genes bchCDIX, pucC2, and pufL related to Bchl a biosynthesis and photosynthetic reaction center assembly. Metagenome-assembled genomes (MAGs) of sorted cells from pelagic seawater and deep-sea hydrothermal sediment belonged to Erythrobacter sanguineus that was considered as an AAPB and genus Sphingomonas, respectively. Moreover, multiple photosynthesis-related genes were annotated in both MAGs, and comparative genomic analysis revealed several exclusive genes involved in amino acid and inorganic ion metabolism and transport. This study employed a new single-cell spectroscopy method to detect AAPB, not only broadening the taxonomic and genetic contents of AAPB in marine environments but also revealing their genetic mechanisms at the single-genomic level.

Soil Bacterial Community Structure in Different Micro-Habitats on the Tidal Creek Section in the Yellow River Estuary

Tidal creeks have attracted considerable attention in estuary wetland conservation and restoration with diverse micro-habitats and high hydrological connectivity. Bacterial communities act effectively as invisible engines to regulate nutrient element biogeochemical processes. However, few studies have unveiled the bacterial community structures and diversities of micro-habitats soils on the tidal creek section. Our study selected three sections cross a tidal creek with obviously belt-like habitats “pluff mudflat – bare mudflat – Tamarix chinensis community – T. chinensis-Suaeda salsa community– S. salsa community” in the Yellow River estuarine wetland. Based on soil samples, we dissected and untangled the bacterial community structures and special bacterial taxa of different habitats on the tidal creek section. The results showed that bacterial community structures and dominant bacterial taxa were significantly different in the five habitats. The bacterial community diversities significantly decreased with distance away from tidal creeks, as well as the dominant bacteria Flavobacteriia and δ-Proteobacteria, but in reverse to Bacteroidetes and Gemmatimonadetes. Moreover, the important biomarkers sulfate-reducing bacteria and photosynthetic bacteria were different distributions within the five habitats, which were closely associated with the sulfur and carbon cycles. We found that the bacterial communities were heterogeneous in different micro-habitats on the tidal creek section, which was related to soil salinity, moisture, and nutrients as well as tidal action. The study would provide fundamental insights into understanding the ecological functions of bacterial diversities and biogeochemical processes influenced by tidal creeks.

Litoreibacter roseus sp. nov., a novel bacteriochlorophyll a-containing bacterium

A strictly aerobic, bacteriochlorophyll (BChl) a-containing alphaproteobacterium, designated strain K6^T, was isolated from seawater around an aquaculture site in the Uwa Sea in Japan. The novel strain grew optimally at 30 °C at pH 7.0-7.5 and in the presence of 2.0 % (w/v) NaCl. The nonmotile and coccoid or rod-shaped cells formed pink-pigmented colonies on agar plates containing organic compounds. Cells showed an in vivo absorption maximum at 870 nm in the near-infrared region, indicating the presence of BChl a in the light-harvesting 1 complex. The new bacterial strain was Gram-stain-negative and oxidase- and catalase-positive. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain K6^T was closely related to species in the genus Litoreibacter. The closest phylogenetic relatives of strain K6^T were Litoreibacter ponti GJSW-31^T (98.56 % sequence similarity), Litoreibacter janthinus KMM 3842^T (97.63 %) and Litoreibacter albidus KMM 3851^T (96.88 %). The G+C content of the genomic DNA was 58.26 mol%. The average nucleotide identity value of strain K6^T with the type strain of L. ponti was 77.16 % (SD 4.79 %). The digital DNA-DNA hybridization value of strain K6^T with the type strain of L. ponti was 19.40 %. The respiratory quinone was ubiquinone-10. The major cellular fatty acids were C_18 : 1 ω7c, C_16 : 0 and 11-methyl C_18 : 1 ω7c. The dominant polar lipids were phosphatidylcholine and phosphatidylglycerol. On the basis of the genetic and phenotypic data obtained in the present study, we propose a new species in the genus Litoreibacter: Litoreibacter roseus sp. nov., whose type strain is K6^T (=DSM 110109^T=NBRC 114114^T). Strain K6^T represents the first confirmed species that produces BChl a within the genus Litoreibacter.

Taxonomic differences shape the responses of freshwater aerobic anoxygenic phototrophic bacterial communities to light and predation

Aerobic anoxygenic phototrophic (AAP) bacteria are a phylogenetically diverse and ubiquitous group of prokaryotes that use organic matter but can harvest light using bacteriochlorophyll a. Although the factors regulating AAP ecology have long been investigated through field surveys, the few available experimental studies have considered AAPs as a group, thus disregarding the potential differential responses between taxonomically distinct AAP assemblages. Here, we used sequencing of the pufM gene to describe the diversity of AAPs in 10 environmentally distinct temperate lakes, and to investigate the taxonomic responses of AAP communities in these lakes when subjected to similar experimental manipulations of light and predator removal. The studied communities were clearly dominated by Limnohabitans AAP but presented a clear taxonomic segregation between lakes presumably driven by local conditions, which was maintained after experimental manipulations. Predation reduction (but not light exposure) caused significant compositional shifts across most assemblages, but the magnitude of these changes could not be clearly related to changes in bulk AAP abundances or taxonomic richness of AAP assemblages during experiments. Only a few operational taxonomic units, which differed taxonomically between lakes, were found to respond positively during experimental treatments. Our results highlight that different freshwater AAP communities respond differently to similar control mechanisms, highlighting that in-depth knowledge on AAP diversity is essential to understand the ecology and potential role of these photoheterotrophs.

Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities

Phototrophic communities of photosynthetic algae or cyanobacteria and heterotrophic bacteria or fungi are pervasive throughout the environment¹. How interactions between members contribute to the resilience and affect the fitness of phototrophic communities is not fully understood^2,3. Here, we integrated metatranscriptomics, metabolomics and phenotyping with computational modelling to reveal condition-dependent secretion and cross-feeding of metabolites in a synthetic community. We discovered that interactions between members are highly dynamic and are driven by the availability of organic and inorganic nutrients. Environmental factors, such as ammonia concentration, influenced community stability by shifting members from collaborating to competing. Furthermore, overall fitness was dependent on genotype and streamlined genomes improved growth of the entire community. Our mechanistic framework provides insights into the physiology and metabolic response to environmental and genetic perturbation of these ubiquitous microbial associations.

Picoplankton Distribution and Activity in the Deep Waters of the Southern Adriatic Sea

Southern Adriatic (Eastern Mediterranean Sea) is a region strongly dominated by large-scale oceanographic processes and local open-ocean dense water formation. In this study, picoplankton biomass, distribution, and activity were examined during two oceanographic cruises and analyzed in relation to environmental parameters and hydrographic conditions comparing pre and post-winter phases (December 2015, April 2016). Picoplankton density with the domination of autotrophic biomasses was higher in the pre-winter phase when significant amounts of picoaoutotrophs were also found in the meso-and bathy-pelagic layers, while Synechococcus dominated the picoautotrophic group. Higher values of bacterial production and domination of High Nucleic Acid content bacteria (HNA bacteria) were found in deep waters, especially during the post-winter phase, suggesting that bacteria can have an active role in the deep-sea environment. Aerobic anoxygenic phototrophic bacteria accounted for a small proportion of total heterotrophic bacteria but contributed up to 4% of bacterial carbon content. Changes in the picoplankton community were mainly driven by nutrient availability, heterotrophic nanoflagellates abundance, and water mass movements and mixing. Our results suggest that autotrophic and heterotrophic members of the picoplankton community are an important carbon source in the food web in the deep-sea, as well as in the epipelagic layer. Besides, viral lysis may affect the activity of the picoplankton community and enrich the water column with dissolved organic carbon.

High temperature accelerates growth of aerobic anoxygenic phototrophic bacteria in seawater

Temperature is an important controlling factor in the growth activity of all microorganisms. Aerobic anoxygenic phototrophic (AAP) bacteria actively grow in the ocean and are known as one of the main driving forces in organic matter cycling in surface seawater environments. Whether temperature change affects AAP bacteria activity from an ecological viewpoint remains an open question. To date, no known studies have reported the effect of temperature change on AAP bacteria growth in the ocean. We here show that the growth rate of AAP bacteria exceeded that of other bacterial types at high water temperatures in the absence of grazers. The slope of the regression line of the net growth rate of AAP bacteria as a function of water temperature was the same as that for non‐AAP bacteria at all temperatures (10, 20, and 30°C); however, when grazers were eliminated, it was 4.7 times higher than that of non‐AAP bacteria. This result suggests that AAP bacteria are more responsive to water temperature increases than other bacteria and that AAP bacteria might become more dominant than other bacteria under elevated water temperatures.

Distribution and Diversity of Rhodopsin-Producing Microbes in the Chesapeake Bay

Although sunlight is an abundant source of energy in surface environments, less than 0.5% of the available photons are captured by (bacterio)chlorophyll-dependent photosynthesis in plants and bacteria. Metagenomic data indicate that 30 to 60% of the bacterial genomes in some environments encode rhodopsins, retinal-based photosystems found in heterotrophs, suggesting that sunlight may provide energy for more life than previously suspected. However, quantitative data on the number of cells that produce rhodopsins in environmental systems are limited. Here, we use total internal reflection fluorescence microscopy to show that the number of free-living microbes that produce rhodopsins increases along the salinity gradient in the Chesapeake Bay. We correlate this functional data with environmental data to show that rhodopsin abundance is positively correlated with salinity and with indicators of active heterotrophy during the day. Metagenomic and metatranscriptomic data suggest that the microbial rhodopsins in the low-salinity samples are primarily found in Actinobacteria and Bacteroidetes, while those in the high-salinity samples are associated with SAR-11 type AlphaproteobacteriaIMPORTANCE Microbial rhodopsins are common light-activated ion pumps in heterotrophs, and previous work has proposed that heterotrophic microbes use them to conserve energy when organic carbon is limiting. If this hypothesis is correct, rhodopsin-producing cells should be most abundant where nutrients are most limited. Our results indicate that in the Chesapeake Bay, rhodopsin gene abundance is correlated with salinity, and functional rhodopsin production is correlated with nitrate, bacterial production, and chlorophyll a We propose that in this environment, where carbon and nitrogen are likely not limiting, heterotrophs do not need to use rhodopsins to supplement ATP synthesis. Rather, the light-generated proton motive force in nutrient-rich environments could be used to power energy-dependent membrane-associated processes, such as active transport of organic carbon and cofactors, enabling these organisms to more efficiently utilize exudates from primary producers.

Isolation and characterization of the first phage infecting ecologically important marine bacteria Erythrobacter

Background

Erythrobacter comprises a widespread and ecologically significant genus of marine bacteria. However, no phage infecting Erythrobacter spp. has been reported to date. This study describes the isolation and characterization of phage vB_EliS-R6L from Erythrobacter.

Methods

Standard virus enrichment and double-layer agar methods were used to isolate and characterize the phage. Morphology was observed by transmission electron microscopy, and a one-step growth curve assay was performed. The phage genome was sequenced using the Illumina Miseq platform and annotated using standard bioinformatics tools. Phylogenetic analyses were performed based on the deduced amino acid sequences of terminase, endolysin, portal protein, and major capsid protein, and genome recruitment analysis was conducted using Jiulong River Estuary Virome, Pacific Ocean Virome and Global Ocean Survey databases.

Results

A novel phage, vB_EliS-R6L, from coastal waters of Xiamen, China, was isolated and found to infect the marine bacterium Erythrobacter litoralis DSM 8509. Morphological observation and genome analysis revealed that phage vB_EliS-R6L is a siphovirus with a 65.7-kb genome that encodes 108 putative gene products. The phage exhibits growth at a wide range of temperature and pH conditions. Genes encoding five methylase-related proteins were found in the genome, and recognition site predictions suggested its resistance to restriction-modification host systems. Genomic comparisons and phylogenetic analyses indicate that phage vB_EliS-R6L is distinct from other known phages. Metagenomic recruitment analysis revealed that vB_EliS-R6L-like phages are widespread in marine environments, with likely distribution in coastal waters.

Conclusions

Isolation of the first Erythrobacter phage (vB_EliS-R6L) will contribute to our understanding of host-phage interactions, the ecology of marine Erythrobacter and viral metagenome annotation efforts.

Light enhances the growth rates of natural populations of aerobic anoxygenic phototrophic bacteria

Aerobic anoxygenic phototrophic (AAP) bacteria are microorganisms that can harvest light energy using bacteriochlorophyll a to supplement their predominantly organotrophic metabolism. Growth enhancement by light has repeatedly been demonstrated in laboratory experiments with AAP isolates. However, the ecological advantage of light utilization is unclear, as it has never been proven in the natural environment. Here, we conducted manipulation experiments in the NW Mediterranean and found that AAP bacteria display high growth rates which are controlled to a large extent by intense grazing pressure and phosphorous availability. Foremost, we found that, contrarily to the bulk bacterioplakton, AAP bacteria display higher growth rates when incubated under light-dark cycles than in complete darkness. These results represent the first direct evidence that natural populations of marine AAP bacteria can be stimulated by light.

Diversity and Distribution of Freshwater Aerobic Anoxygenic Phototrophic Bacteria across a Wide Latitudinal Gradient

Aerobic anoxygenic phototrophs (AAPs) have been shown to exist in numerous marine and brackish environments where they are hypothesized to play important ecological roles. Despite their potential significance, the study of freshwater AAPs is in its infancy and limited to local investigations. Here, we explore the occurrence, diversity and distribution of AAPs in lakes covering a wide latitudinal gradient: Mongolian and German lakes located in temperate regions of Eurasia, tropical Great East African lakes, and polar permanently ice-covered Antarctic lakes. Our results show a widespread distribution of AAPs in lakes with contrasting environmental conditions and confirm that this group is composed of different members of the Alpha- and Betaproteobacteria. While latitude does not seem to strongly influence AAP abundance, clear patterns of community structure and composition along geographic regions were observed as indicated by a strong macro-geographical signal in the taxonomical composition of AAPs. Overall, our results suggest that the distribution patterns of freshwater AAPs are likely driven by a combination of small-scale environmental conditions (specific of each lake and region) and large-scale geographic factors (climatic regions across a latitudinal gradient).

Abundance of Common Aerobic Anoxygenic Phototrophic Bacteria in a Coastal Aquaculture Area

Aerobic anoxygenic phototrophic bacteria (AAnPB) rely on not only heterotrophic but also phototrophic energy gain. AAnPB are known to have high abundance in oligotrophic waters and are the major portion of the bacterial carbon stock in the environment. In a yearlong study in an aquaculture area in the Uwa Sea, Japan, AAnPB, accounted for 4.7 to 24% of the total bacteria by count. Since the cell volume of AAnPB is 2.23 ± 0.674 times larger than the mean for total bacteria, AAnPB biomass is estimated to account for 10–53% of the total bacterial assemblage. By examining pufM gene sequence, a common phylogenetic AAnPB species was found in all sampling sites through the year. The common species and other season-specific species were phylogenetically close to unculturable clones recorded in the Sargasso Sea and Pacific Ocean. The present study suggests that the common species may be a cosmopolitan species with worldwide distribution that is abundant not only in the oligotrophic open ocean but also in eutrophic aquaculture areas.

Geographic Impact on Genomic Divergence as Revealed by Comparison of Nine Citromicrobial Genomes

Aerobic anoxygenic phototrophic bacteria (AAPB) are thought to be important players in oceanic carbon and energy cycling in the euphotic zone of the ocean. The genus Citromicrobium, widely found in oligotrophic oceans, is a member of marine alphaproteobacterial AAPB. Nine Citromicrobium strains isolated from the South China Sea, the Mediterranean Sea, or the tropical South Atlantic Ocean were found to harbor identical 16S rRNA sequences. The sequencing of their genomes revealed high synteny in major regions. Nine genetic islands (GIs) involved mainly in type IV secretion systems, flagellar biosynthesis, prophage, and integrative conjugative elements, were identified by a fine-scale comparative genomics analysis. These GIs played significant roles in genomic evolution and divergence. Interestingly, the coexistence of two different photosynthetic gene clusters (PGCs) was not only found in the analyzed genomes but also confirmed, for the first time, to our knowledge, in environmental samples. The prevalence of the coexistence of two different PGCs may suggest an adaptation mechanism for Citromicrobium members to survive in the oceans. Comparison of genomic characteristics (e.g., GIs, average nucleotide identity [ANI], single-nucleotide polymorphisms [SNPs], and phylogeny) revealed that strains within a marine region shared a similar evolutionary history that was distinct from that of strains isolated from other regions (South China Sea versus Mediterranean Sea). Geographic differences are partly responsible for driving the observed genomic divergences and allow microbes to evolve through local adaptation. Three Citromicrobium strains isolated from the Mediterranean Sea diverged millions of years ago from other strains and evolved into a novel group.

IMPORTANCE

Aerobic anoxygenic phototrophic bacteria are a widespread functional group in the upper ocean, and their abundance could be up to 15% of the total heterotrophic bacteria. To date, a great number of studies display AAPB biogeographic distribution patterns in the ocean; however, little is understood about the geographic isolation impact on the genome divergence of marine AAPB. In this study, we compare nine Citromicrobium genomes of strains that have identical 16S rRNA sequences but different ocean origins. Our results reveal that strains isolated from the same marine region share a similar evolutionary history that is distinct from that of strains isolated from other regions. These Citromicrobium strains diverged millions of years ago. In addition, the coexistence of two different PGCs is prevalent in the analyzed genomes and in environmental samples.

High turnover rates of aerobic anoxygenic phototrophs in European freshwater lakes

Aerobic Anoxygenic Phototrophic (AAP) bacteria are bacteriochlorophyll (BChl) a -containing organisms which use light energy to supplement their predominantly heterotrophic metabolism. Here, we investigated mortality and growth rates of AAP bacteria in three different freshwater lakes in Central Europe: the mountain lake Plešné, the oligo-mesotrophic Lake Stechlin and the forest pond Huntov. The mortality of AAP bacteria was estimated from diel changes of BChl a fluorescence. Net and gross growth rates were calculated from the increases in AAP cell numbers. The gross growth rates of AAP bacteria ranged from 0.38 to 5.6 d^-1 , with the highest values observed during summer months. Simultaneously, the rapidly growing AAP cells have to cope with an intense grazing pressure by both zooplankton and protists. The presented results document that during the day, gross growth usually surpased mortality. Our results indicate that AAP bacteria utilize light energy under natural conditions to maintain rapid growth rates, which are balanced by a generally intense grazing pressure.

Spatial and temporal variability of aerobic anoxygenic photoheterotrophic bacteria along the east coast of Australia

Aerobic Anoxygenic Phototrophic Bacteria (AAnPB) are ecologically important microorganisms, widespread in oceanic photic zones. However, the key environmental drivers underpinning AAnPB abundance and diversity are still largely undefined. The temporal patterns in AAnPB dynamics at three oceanographic reference stations spanning at approximately 15° latitude along the Australian east coast were examined. AAnPB abundance was highly variable, with pufM gene copies ranging from 1.1 × 10² to 1.4 × 10⁵ ml^-1 and positively correlated with day length and solar radiation. pufM gene Miseq sequencing revealed that the majority of sequences were closely related to those obtained previously, suggesting that key AAnPB groups are widely distributed across similar environments globally. Temperature was a major structuring factor for AAnPB assemblages across large spatial scales, correlating positively with richness and Gammaproteobacteria (phylogroup K) abundance but negatively with Roseobacter-clade (phylogroup E) abundance, with temperatures between 16°C and 18°C identified as a potential transition zone between these groups. Network analysis revealed that discrete AAnPB populations exploit specific niches defined by varying temperature, light and nutrient conditions in the Tasman Sea system, with evidence for both niche sharing and partitioning amongst closely related operational taxonomic units.

A Comparison of 14 Erythrobacter Genomes Provides Insights into the Genomic Divergence and Scattered Distribution of Phototrophs

Aerobic anoxygenic phototrophic bacteria (AAPB) are bacteriochlorophyll a (Bchl a)-containing microbial functional population. Erythrobacter is the first genus that was identified to contain AAPB species. Here, we compared 14 Erythrobacter genomes: seven phototrophic strains and seven non- phototrophic strains. Interestingly, AAPB strains are scattered in this genus based on their phylogenetic relationships. All 14 strains could be clustered into three groups based on phylo-genomic analysis, average genomic nucleotide identity and the phylogeny of signature genes (16S rRNA and virB4 genes). The AAPB strains were distributed in three groups, and gain and loss of phototrophic genes co-occurred in the evolutionary history of the genus Erythrobacter. The organization and structure of photosynthesis gene clusters (PGCs) in seven AAPB genomes displayed high synteny of major regions except for few insertions. The 14 Erythrobacter genomes had a large range of genome sizes, from 2.72 to 3.60 M, and the sizes of the core and pan- genomes were 1231 and 8170 orthologous clusters, respectively. Integrative and conjugative elements (ICEs) were frequently identified in genomes we studied, which might play significant roles in shaping or contributing to the pan-genome of Erythrobacter. Our findings suggest the ongoing evolutionary divergence of Erythrobacter genomes and the scattered distribution characteristic of PGC.

Seasonal Succession Leads to Habitat-Dependent Differentiation in Ribosomal RNA:DNA Ratios among Freshwater Lake Bacteria

Relative abundance profiles of bacterial populations measured by sequencing DNA or RNA of marker genes can widely differ. These differences, made apparent when calculating ribosomal RNA:DNA ratios, have been interpreted as variable activities of bacterial populations. However, inconsistent correlations between ribosomal RNA:DNA ratios and metabolic activity or growth rates have led to a more conservative interpretation of this metric as the cellular protein synthesis potential (PSP). Little is known, particularly in freshwater systems, about how PSP varies for specific taxa across temporal and spatial environmental gradients and how conserved PSP is across bacterial phylogeny. Here, we generated 16S rRNA gene sequencing data using simultaneously extracted DNA and RNA from fractionated (free-living and particulate) water samples taken seasonally along a eutrophic freshwater estuary to oligotrophic pelagic transect in Lake Michigan. In contrast to previous reports, we observed frequent clustering of DNA and RNA data from the same sample. Analysis of the overlap in taxa detected at the RNA and DNA level indicated that microbial dormancy may be more common in the estuary, the particulate fraction, and during the stratified period. Across spatiotemporal gradients, PSP was often conserved at the phylum and class levels. PSPs for specific taxa were more similar across habitats in spring than in summer and fall. This was most notable for PSPs of the same taxa when located in the free-living or particulate fractions, but also when contrasting surface to deep, and estuary to Lake Michigan communities. Our results show that community composition assessed by RNA and DNA measurements are more similar than previously assumed in freshwater systems. However, the similarity between RNA and DNA measurements and taxa-specific PSPs that drive community-level similarities are conditional on spatiotemporal factors.

Single-cell activity of freshwater aerobic anoxygenic phototrophic bacteria and their contribution to biomass production

Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophs that despite their low abundances have been hypothesized to play an ecologically and biogeochemically important role in aquatic systems. Characterizing this role requires a better understanding of the in situ dynamics and activity of AAP bacteria. Here we provide the first assessment of the single-cell activity of freshwater AAP bacteria and their contribution to total bacterial production across lakes spanning a wide trophic gradient, and explore the role of light in regulating AAP activity. The proportion of cells that were active in leucine incorporation and the level of activity per cell were consistently higher for AAP than for bulk bacteria across lakes. As a result, AAP bacteria contributed disproportionately more to total bacterial production than to total bacterial abundance. Interestingly, although environmentally driven patterns in activity did not seem to differ largely between AAP and bulk bacteria, their response to light did, and exposure to light resulted in increases in the proportion of active AAP bacteria with no clear effect on their cell-specific activity. This suggests that light may play a role in the activation of AAP bacteria, enabling these photoheterotrophs to contribute more to the carbon cycle than suggested by their abundance.

Growth Rates of Microbes in the Oceans

A microbe's growth rate helps to set its ecological success and its contribution to food web dynamics and biogeochemical processes. Growth rates at the community level are constrained by biomass and trophic interactions among bacteria, phytoplankton, and their grazers. Phytoplankton growth rates are approximately 1 d(-1), whereas most heterotrophic bacteria grow slowly, close to 0.1 d(-1); only a few taxa can grow ten times as fast. Data from 16S rRNA and other approaches are used to speculate about the growth rate and the life history strategy of SAR11, the most abundant clade of heterotrophic bacteria in the oceans. These strategies are also explored using genomic data. Although the methods and data are imperfect, the available data can be used to set limits on growth rates and thus on the timescale for changes in the composition and structure of microbial communities.

Patterns in Abundance, Cell Size and Pigment Content of Aerobic Anoxygenic Phototrophic Bacteria along Environmental Gradients in Northern Lakes

There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex.