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  1. Abstract Ecological network analyses are used to identify potential biotic interactions between microorganisms from species abundance data. These analyses are often carried out using time-series data; however, time-series networks have unique statistical challenges. Time-dependent species abundance data can lead to species co-occurrence patterns that are not a result of direct, biotic associations and may therefore result in inaccurate network predictions. Here, we describe a generalize additive model (GAM)-based data transformation that removes time-series signals from species abundance data prior to running network analyses. Validation of the transformation was carried out by generating mock, time-series datasets, with an underlying covariance structure, running network analyses on these datasets with and without our GAM transformation, and comparing the network outputs to the known covariance structure of the simulated data. The results revealed that seasonal abundance patterns substantially decreased the accuracy of the inferred networks. In addition, the GAM transformation increased the predictive power (F1 score) of inferred ecological networks on average and improved the ability of network inference methods to capture important features of network structure. This study underscores the importance of considering temporal features when carrying out network analyses and describes a simple, effective tool that can be used to improve results. 
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  2. Abstract

    Marine snow and other particles are abundant in estuaries, where they drive biogeochemical transformations and elemental transport. Particles range in size, thereby providing a corresponding gradient of habitats for marine microorganisms. We used standard normalized amplicon sequencing, verified with microscopy, to characterize taxon‐specific microbial abundances, (cells per litre of water and per milligrams of particles), across six particle size classes, ranging from 0.2 to 500 μm, along the main stem of the Chesapeake Bay estuary. Microbial communities varied in salinity, oxygen concentrations, and particle size. Many taxonomic groups were most densely packed on large particles (in cells/mg particles), yet were primarily associated with the smallest particle size class, because small particles made up a substantially larger portion of total particle mass. However, organisms potentially involved in methanotrophy, nitrite oxidation, and sulphate reduction were found primarily on intermediately sized (5–180 μm) particles, where species richness was also highest. All abundant ostensibly free‐living organisms, including SAR11 andSynecococcus, appeared on particles, albeit at lower abundance than in the free‐living fraction, suggesting that aggregation processes may incorporate them into particles. Our approach opens the door to a more quantitative understanding of the microscale and macroscale biogeography of marine microorganisms.

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  3. Abstract. Recent earth system models predict a 10 %–20 % decrease in particulate organic carbon export from the surface ocean by the end of the21st century due to global climate change. This decline is mainly caused by increased stratification of the upper ocean, resulting in reducedshallow subsurface nutrient concentrations and a slower supply of nutrients to the surface euphotic zone in low latitudes. These predictions,however, do not typically account for associated changes in remineralization depths driven by sinking-particle size. Here we combinesatellite-derived export and particle size maps with a simple 3-D global biogeochemical model that resolves dynamic particle size distributions toinvestigate how shifts in particle size may buffer or amplify predicted changes in surface nutrient supply and therefore export production. We showthat higher export rates are empirically correlated with larger sinking particles and presumably larger phytoplankton, particularly in tropical andsubtropical regions. Incorporating these empirical relationships into our global model shows that as circulation slows, a decrease in export isassociated with a shift towards smaller particles, which sink more slowly and are thus remineralized shallower. This shift towards shallowerremineralization in turn leads to greater recycling of nutrients in the upper water column and thus faster nutrient recirculation into the euphoticzone. The end result is a boost in productivity and export that counteracts the initial circulation-driven decreases. This negative feedbackmechanism (termed the particle-size–remineralization feedback) slows export decline over the next century by ∼ 14 % globally (from −0.29to −0.25 GtC yr−1) and by ∼ 20 % in the tropical and subtropical oceans, where export decreases are currently predicted tobe greatest. Our findings suggest that to more accurately predict changes in biological pump strength under a warming climate, earth system modelsshould include dynamic particle-size-dependent remineralization depths. 
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  4. Abstract

    In lakes, seasonal phytoplankton blooms and allochthonous plant debris intensify particulate organic carbon fluxes to the lakebed. Microbes associated with these particles likely vary with organic substrate lability and redox conditions. To explore microbial compositional responses to these variables, we analyzed particle‐associated and free‐living assemblages in the permanently redox‐stratified Fayetteville Green Lake using 16 S rRNA amplicon sequencing during the peak and end of cyanobacterial and photoautotrophic sulfur bacterial blooms. Assemblage compositions were strongly influenced by redox conditions and particle association. Assemblage compositions varied seasonally above the lower oxycline boundary (summer—generalist heterotrophs; autumn—iron reducers and specialist heterotrophs), but not in the anoxic region below. Particle‐associated assemblages were less diverse than free‐living assemblages and were dominated by heterotrophs that putatively metabolize complex organic substrates, purple sulfur bacteria, sulfur‐cyclingDesulfocapsa, and eukaryotic algae. The least diverse particle‐associated assemblages occurred near the lower oxycline boundary, where microbial activities and abundances were highest, and anoxygenic photoautotrophs were enriched. The low‐diversity particle‐associated heterotrophs likely remineralize complex organic substrates, releasing simpler organic substrates to free‐living assemblages during transit, thereby influencing surrounding microbial diversity and function. Our results challenge the paradigm that phytoplankton from the shallow photic zone are the primary contributor to the vertical flux. We suggest that photoautotrophic prokaryotes from the deep photic zone contribute significantly to deep‐water carbon in this environment, and possibly in other oxygen‐deficient waters with sulfidic photic zones. Furthermore, results suggest that seasonally variable terrestrial carbon and metal inputs also influence microbial diversity and function in similar systems.

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  5. Abstract

    Short timescale observations are valuable for understanding microbial ecological processes. We assessed dynamics in relative abundance and potential activities by sequencing the small sub-unit ribosomal RNA gene (rRNA gene) and rRNA molecules (rRNA) of Bacteria, Archaea, and Eukaryota once to twice daily between March 2014 and May 2014 from the surface ocean off Catalina Island, California. Typically Ostreococcus, Braarudosphaera, Teleaulax, and Synechococcus dominated phytoplankton sequences (including chloroplasts) while SAR11, Sulfitobacter, and Fluviicola dominated non-phytoplankton Bacteria and Archaea. We observed short-lived increases of diatoms, mostly Pseudo-nitzschia and Chaetoceros, with quickly responding Bacteria and Archaea including Flavobacteriaceae (Polaribacter & Formosa), Roseovarius, and Euryarchaeota (MGII), notably the exact amplicon sequence variants we observed responding similarly to another diatom bloom nearby, 3 years prior. We observed correlations representing known interactions among abundant phytoplankton rRNA sequences, demonstrating the biogeochemical and ecological relevance of such interactions: (1) The kleptochloroplastidic ciliate Mesodinium 18S rRNA gene sequences and a single Teleaulax taxon (via 16S rRNA gene sequences) were correlated (Spearman r = 0.83) yet uncorrelated to a Teleaulax 18S rRNA gene OTU, or any other taxon (consistent with a kleptochloroplastidic or karyokleptic relationship) and (2) the photosynthetic prymnesiophyte Braarudosphaera bigelowii and two strains of diazotrophic cyanobacterium UCYN-A were correlated and each taxon was also correlated to other taxa, including B. bigelowii to a verrucomicrobium and a dictyochophyte phytoplankter (all r > 0.8). We also report strong correlations (r > 0.7) between various ciliates, bacteria, and phytoplankton, suggesting interactions via currently unknown mechanisms. These data reiterate the utility of high-frequency time series to show rapid microbial reactions to stimuli, and provide new information about in situ dynamics of previously recognized and hypothesized interactions.

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  6. Abstract

    Models and observations suggest that particle flux attenuation is lower across the mesopelagic zone of anoxic environments compared to oxic environments. Flux attenuation is controlled by microbial metabolism as well as aggregation and disaggregation by zooplankton, all of which shape the relative abundance of differently sized particles. Observing and modeling particle spectra can provide information about the contributions of these processes. We measured particle size spectrum profiles at one station in the oligotrophic Eastern Tropical North Pacific Oxygen Deficient Zone (ETNP ODZ) using an underwater vision profiler (UVP), a high‐resolution camera that counts and sizes particles. Measurements were taken at different times of day, over the course of a week. Comparing these data to particle flux measurements from sediment traps collected over the same time‐period allowed us to constrain the particle size to flux relationship, and to generate highly resolved depth and time estimates of particle flux rates. We found that particle flux attenuated very little throughout the anoxic water column, and at some time points appeared to increase. Comparing our observations to model predictions suggested that particles of all sizes remineralize more slowly in the ODZ than in oxic waters, and that large particles disaggregate into smaller particles, primarily between the base of the photic zone and 500 m. Acoustic measurements of multiple size classes of organisms suggested that many organisms migrated, during the day, to the region with high particle disaggregation. Our data suggest that diel‐migrating organisms both actively transport biomass and disaggregate particles in the ODZ core.

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