Heterotrophic Bacterial Community Research Articles

Full-length 16S rRNA gene sequencing reveals the operating mode and chlorination-aggravated SWRO biofouling at a nuclear power plant.

Reverse osmosis (RO) membrane fouling and biological contamination problems faced by seawater desalination systems are microbiologically related. We used full-length 16S rRNA gene sequencing to assess the bacterial community structure and chlorine-resistant bacteria (CRB) associated with biofilm growth in different treatment processes under the winter mode of a chlorinated seawater desalination system in China. At the outset of the winter mode, certain CRB, such as Acinetobacter, Pseudomonas, and Bacillus held sway over the bacterial community structure, playing a pivotal role in biofouling. At the mode's end, Deinococcus and Paracoccus predominated, with Pseudomonas and Roseovarius following suit, while certain CRB genera still maintained their dominance. RO and chlorination are pivotal factors in shaping the bacterial community structure and diversity, and increases in total heterotrophic bacterial counts and community diversity in safety filters may adversely affect the effectiveness of subsequent RO systems. Besides, the bacterial diversity and culturable biomass in the water produced by the RO system remain high, and some conditionally pathogenic CRBs pose a certain microbial risk as a source of drinking water. Targeted removal of these CRBs will be an important area of research for advancing control over membrane clogging and ensuring water quality safety in the future.

Interaction between phytoplankton and heterotrophic bacteria in Arctic fjords during the glacial melting season as revealed by eDNA metabarcoding.

The hydrographic variability in the fjords of Svalbard significantly influences water mass properties, causing distinct patterns of microbial diversity and community composition between surface and subsurface layers. However, surveys on the phytoplankton-associated bacterial communities, pivotal to ecosystem functioning in Arctic fjords, are limited. This study investigated the interactions between phytoplankton and heterotrophic bacterial communities in Svalbard fjord waters through comprehensive eDNA metabarcoding with 16S and 18S rRNA genes. The 16S rRNA sequencing results revealed a homogenous community composition including a few dominant heterotrophic bacteria across fjord waters, whereas 18S rRNA results suggested a spatially diverse eukaryotic plankton distribution. The relative abundances of heterotrophic bacteria showed a depth-wise distribution. By contrast, the dominant phytoplankton populations exhibited variable distributions in surface waters. In the network model, the linkage of phytoplankton (Prasinophytae and Dinophyceae) to heterotrophic bacteria, particularly Actinobacteria, suggested the direct or indirect influence of bacterial contributions on the fate of phytoplankton-derived organic matter. Our prediction of the metabolic pathways for bacterial activity related to phytoplankton-derived organic matter suggested competitive advantages and symbiotic relationships between phytoplankton and heterotrophic bacteria. Our findings provide valuable insights into the response of phytoplankton-bacterial interactions to environmental changes in Arctic fjords.

Viral infection of an estuarine Synechococcus influences its co-occurring heterotrophic bacterial community in the culture.

Viruses are infectious and abundant in the marine environment. Viral lysis of host cells releases organic matter and nutrients that affect the surrounding microbial community. Synechococcus are important primary producers in the ocean and they are subject to frequent viral infection. In the laboratory, Synechococcus cultures are often associated with bacteria and such a co-existence relationship appears to be important to the growth and stability of Synechococcus. However, we know little about how viral lysis of Synechococcus affects the co-existing bacteria in the culture. This study investigated the influence of viral infection of Synechococcus on co-occurring bacterial community in the culture. We analyzed the community composition, diversity, predicted functions of the bacterial community, and its correlations with fluorescent dissolved organic matter (FDOM) components and nutrients after introducing a cyanophage to the Synechococcus culture. Cyanophage infection altered the bacterial community structure and increased the bacterial diversity and richness. Increased bacterial groups such as Bacteroidetes and Alphaproteobacteria and decreased bacterial groups such as Gammaproteobacteria were observed. Moreover, cyanophage infection reduced bacterial interactions but enhanced correlations between the dominant bacterial taxa and nutrients. Unique FDOM components were observed in the cyanophage-added culture. Fluorescence intensities of FDOM components varied across the cyanophage-infection process. Decreased nitrate and increased ammonium and phosphate in the cyanophage-added culture coupled with the viral progeny production and increased substance transport and metabolism potentials of the bacterial community. Furthermore, increased potentials in methane metabolism and aromatic compound degradation of the bacterial community were observed in the cyanophage-added culture, suggesting that cyanophage infections contribute to the production of methane-related compounds and refractory organic matter in a microcosm like environment. This study has the potential to deepen our understanding of the impact of viral lysis of cyanobacteria on microbial community in the surrounding water.

Iron limitation of heterotrophic bacteria in the California Current System tracks relative availability of organic carbon and iron.

Iron is an essential nutrient for all microorganisms of the marine environment. Iron limitation of primary production has been well documented across a significant portion of the global surface ocean, but much less is known regarding the potential for iron limitation of the marine heterotrophic microbial community. In this work, we characterize the transcriptomic response of the heterotrophic bacterial community to iron additions in the California Current System, an eastern boundary upwelling system, to detect in situ iron stress of heterotrophic bacteria. Changes in gene expression in response to iron availability by heterotrophic bacteria were detected under conditions of high productivity when carbon limitation was relieved but when iron availability remained low. The ratio of particulate organic carbon to dissolved iron emerged as a biogeochemical proxy for iron limitation of heterotrophic bacteria in this system. Iron stress was characterized by high expression levels of iron transport pathways and decreased expression of iron-containing enzymes involved in carbon metabolism, where a majority of the heterotrophic bacterial iron requirement resides. Expression of iron stress biomarkers, as identified in the iron-addition experiments, was also detected insitu. These results suggest iron availability will impact the processing of organic matter by heterotrophic bacteria with potential consequences for the marine biological carbon pump.

Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation

Traditional culture techniques usually retrieve a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean. Here, we examined the fraction of heterotrophic bacterial communities in photic and deep ocean layers that could be recovered by culture-dependent techniques at a large scale. We compared 16S rRNA gene sequences from a collection of 2003 cultured heterotrophic marine bacteria with global 16S rRNA metabarcoding datasets (16S TAGs) covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 23 samples used for isolation. These global datasets represent 60 322 unique 16S amplicon sequence variants (ASVs). Our results reveal a significantly higher proportion of isolates identical to ASVs in deeper ocean layers reaching up to 28% of the 16S TAGs of the bathypelagic microbial communities, which included the isolation of 3 of the top 10 most abundant 16S ASVs in the global bathypelagic ocean, related to the genera Sulfitobacter, Halomonas and Erythrobacter. These isolates contributed differently to the prokaryotic communities across different plankton size fractions, recruiting between 38% in the free-living fraction (0.2–0.8 µm) and up to 45% in the largest particles (20–200 µm) in the bathypelagic ocean. Our findings support the hypothesis that sinking particles in the bathypelagic act as resource-rich habitats, suitable for the growth of heterotrophic bacteria with a copiotroph lifestyle that can be cultured, and that these cultivable bacteria can also thrive as free-living bacteria.

Diversity of complex polysaccharide degrading bacteria from the sediments of interlinked high Arctic fjords, Svalbard

Polysaccharides comprise a major component of marine organic matter and are mostly produced by phytoplankton through primary production. The present study reports the polysaccharide degrading ability of cold-adapted heterotrophs from interlinked high Arctic fjords in the Svalbard archipelago. One hundred and ninety-five polysaccharide degrading bacteria isolated from inner and outer fjord sediments, 148 bacterial isolates showed complex polysaccharide degrading enzyme activity. Pectinase was the most predominant polysaccharide-degrading enzyme, followed by agarase, alginate lyase, chitinase, and laminarinase. Xylanase and carboxy methyl cellulase were showed in a relatively lesser activity. Heterotrophic bacterial isolates from the inner and outer shelf regions showed variation in their complex polysaccharide utilization ability. In Kongsfjorden, pectinase producing bacteria were more prevalent in the outer fjord, while chitinase producing bacteria dominated the inner fjord. In Krossfjorden, chitinase producing bacteria were frequently encountered in the outer fjord, whereas pectinase, laminarinase, and alginate lyase producing bacteria dominated the inner fjord. The results of the study indicated that a significant difference in polysaccharide-degrading bacterial phylotypes between the inner and outer fjords (p<0.05). Major polysaccharide-degrading bacteria belonged to phylum Proteobacteria, followed by Firmicutes, Actinobacteria, and Bacteroidetes. The dominant polysaccharide-degrading genera are Marinobacter, Bacillus, Salinibacterium, Alcaligenes, and Planococcus. The findings reveal the availability of a wide range of polysaccharide substrates in fjord sediments and the significant functional role of the heterotrophic bacterial community in the remineralization process of fjord environments.

Analysis of bacterioplankton genes in an impaired Great Lakes harbour reveals seasonal metabolic shifts and a previously undetected cyanobacterium.

Hamilton Harbour is an impaired embayment of Lake Ontario that experiences seasonal algal blooms despite decades of remedial efforts. To study the harbour's cyanobacterial and heterotrophic bacterial communities, we extracted and sequenced community DNA from surface water samples collected biweekly from different sites during summer and fall. Assembled contigs were annotated at the phylum level, and Cyanobacteria were further characterized at order and species levels. Actinobacteria were most abundant in early summer, while Cyanobacteria were dominant in mid-summer. Microcystis aeruginosa and Limnoraphis robusta were most abundant throughout the sampling period, expanding the documented diversity of Cyanobacteria in Hamilton Harbour. Functional annotations were performed using the MG-RAST pipeline and SEED database, revealing that genes for photosynthesis, nitrogen metabolism, and aromatic compound metabolism varied in relative abundances over the season, while phosphorus metabolism was consistent, suggesting that these genes remained essential despite fluctuating environmental conditions and community succession. We observed seasonal shifts from anoxygenic to oxygenic phototrophy, and from ammonia assimilation to nitrogen fixation, coupled with decreasing heterotrophic bacteria and increasing Cyanobacteria relative abundances. Our data contribute important insights into bacterial taxa and functional potentials in Hamilton Harbour, revealing seasonal and spatial dynamics that can be used to inform ongoing remediation efforts.

Enhancement of iron-based nitrogen removal with an electric-magnetic field in an upflow microaerobic sludge reactor (UMSR).

Traditional denitrification often produces high operating costs and excessive sludge disposal expenses due to conventional carbon sources. A novel electric-magnetic field (MF) 48 mT with Fe0 and C-Fe0 powder in an upflow microaerobic sludge reactor (UMSR) improved nitrogen removal from wastewater without organic carbon resources and gave richness to the heterotrophic bacterial community. In the current study, the reactor was operated for 78 ± 2days, divided into five stages (without Fe0, with Fe0, coupling with MF, without coupling with MF, and coupling with MF again), at a hydraulic retention time (HRT) of 2.5h, with an influent loading of ammonium (NH4+-N) 50 ± 2mg/L, at 25-27°C, and less than 1.0mg/L dissolved oxygen (DO). The results demonstrated nitrogen removal efficiency enhanced after coupling with MF on the levels of NO3--N by 76% with an effluent concentration of 8.7mg/L, NH4+-N by 72% with an effluent concentration of 13.6mg/L, and total nitrogen removal (TN) by 76%, respectively. After coupling the MF with the reactor, the microbial community data analysis showed the dominant abundance of ammonia-oxidizing bacteria, heterotrophic nitrifying bacteria, and denitrifying bacteria on the level of Anaerolineaceae_uncultured 2%, which is capable of denitrification that uses Fe2+ as an electron source, Gemmatimonadaceae_uncultured 4%, Hydrogenophaga 4% which is capable of catalyzing hydrogenotrophic denitrification and correlating to nitrate removal, denitrification and desulfurization bacteria SBR1031_norank 18%, anammox-bacteria Saccharimonadales_norank 2%, and (AOM) Limnobacter 3% in the sludge.

Effect of experimentally increased nutrient availability on the structure, metabolic activities, and potential microbial functions of a maritime Antarctic microbial mat.

The role of competitive interactions based on resource utilisation was explored in a phototrophic microbial mat from Byers Peninsula (Maritime Antarctica). Shotgun metagenomic profiling of the mat showed a taxonomic and functionally diverse microbial community. The heterotrophic bacterial community was dominated by Proteobacteria, where genera typically found in polar habitats, such as Janthinobacterium, Pseudomonas, and Polaromonas, were highly prevalent. Cyanobacteria played the main role as primary producers, accompanied by diatoms and chlorophytes. To test the potential effects of the inorganic nutrient (N and P) availability on this community, a fully factorial nitrate and phosphorus addition experiment was conducted in situ. The mat exhibited a functional and structural response to the nutrient amendments. Compared to the undisturbed mat, phosphorus fertilisation favoured the growth of (non-heterocystous) cyanobacteria relative to that of diatoms, as indicated by changes in the carotenoid pigment biomarkers. Although no mat accretion was visible, fertilisation improved the phototrophic activity, and, mainly, when P was amended, the production of exopolymeric substances was favoured, whereas further changes in the vertical distribution of primary production activity were observed as well. Illumina amplicon sequencing of the 16S rRNA gene also demonstrated changes in the relative abundance of heterotrophic prokaryotes, which were detectable from the phylum to the genus level and mainly related to the amendment of nitrogen. Predictions made on the functional skills of these shifted prokaryotic communities indicated changes in abundance selecting taxa with a metabolic adaptation to the new nutrient scenarios. They mainly consisted of the enhancement of ecological strategies and metabolic regulatory mechanisms related to the uptake and metabolising of either nitrogen or phosphorus, regulated by its availability whether in a balanced way or not. This study is a pioneer in demonstrating how shifts in the regional dynamic of nutrients might alter the metabolic equilibrium of these initially considered homeostatic benthic communities. They can be accordingly considered as taxonomically diverse microbiomes with a functional repertoire still inclined to respond to the biogeochemical alteration of nutrient cycles, although occurring in a cold extreme environment where biological activity is partially restricted by environmental harshness.

Novel Interactions Between Phytoplankton and Bacteria Shape Microbial Seasonal Dynamics in Coastal Ocean Waters

Trophic interactions between marine phytoplankton and heterotrophic bacteria are at the base of the biogeochemical carbon cycling in the ocean. However, the specific interactions taking place between phytoplankton and bacterial taxa remain largely unexplored, particularly out of phytoplankton blooming events. Here, we applied network analysis to a 3.5-year time-series dataset to assess the specific associations between different phytoplankton and bacterial taxa along the seasonal scale, distinguishing between free-living and particle-attached bacteria. Using a newly developed network post-analysis technique we removed bacteria-phytoplankton correlations that were primarily driven by environmental parameters, to detect potential biotic interactions. Our results indicate that phytoplankton dynamics may be a strong driver of the inter-annual variability in bacterial community composition. We found the highest abundance of specific bacteria-phytoplankton associations in the particle-attached fraction, indicating a tighter bacteria-phytoplankton association than in the free-living fraction. In the particle-associated fraction we unveiled novel potential associations such as the one between Planctomycetes taxa and the diatom Leptocylindrus spp. Consistent correlations were also found between free-living bacterial taxa and different diatoms, including novel associations such as those between SAR11 with Naviculales diatom order, and between Actinobacteria and Cylindrotheca spp. We also confirmed previously known associations between Rhodobacteraceae and Thalassiosira spp. Our results expand our view on bacteria-phytoplankton associations, suggesting that taxa-specific interactions may largely impact the seasonal dynamics of heterotrophic bacterial communities.

Exploring the Antibiotic Production Potential of Heterotrophic Bacterial Communities Isolated from the Marine Sponges Crateromorpha meyeri, Pseudaxinella reticulata, Farrea similaris, and Caulophacus arcticus through Synergistic Metabolomic and Genomic Analyses.

The discovery of novel secondary metabolites is actively being pursued in new ecosystems. Sponge-associated bacteria have been in the limelight in recent years on account of their ability to produce bioactive compounds. In this study, heterotrophic bacteria associated with four sponge species were isolated, taxonomically identified, and subjected to screening for the production of bioactive entities against a panel of nine microorganisms, including Gram-positive and negative bacteria, as well as yeast and fungi. Of the 105 isolated strains, 66% were represented by Proteobacteria, 16% by Bacteriodetes, 7% by Actinobacteria, and 11% by Firmicutes. Bioactivity screening revealed that 40% of the total isolated strains showed antimicrobial activity against one or more of the target microorganisms tested. Further, active extracts from selective species were narrowed down by bioassay-guided fractionation and subsequently identified by HR-ESI-MS analyses to locate the active peaks. Presumably responsible compounds for the observed bioactivities were identified as pentadecenoic acid, oleic acid, and palmitoleic acid. One isolate, Qipengyuania pacifica NZ-96T, based on 16S rRNA novelty, was subjected to comparative metabolic reconstruction analysis with its closest phylogenetic neighbors, revealing 79 unique functional roles in the novel isolate. In addition, genome mining of Qipengyuania pacifica NZ-96T revealed three biosynthetic gene clusters responsible for the biosynthesis of terpene, beta lactone, lasso peptide, and hserlactone secondary metabolites. Our results demonstrate the ability to target the sponge microbiome as a potential source of novel microbial life with biotechnological potential.

Organic matter availability drives the spatial variation in the community composition and activity of Antarctic marine bacterioplankton.

Carbon cycling by Antarctic microbial plankton is poorly understood but it plays a major role in CO2 sequestration in the Southern Ocean. We investigated the summer bacterioplankton community in the largely understudied Weddell Sea, applying Illumina amplicon sequencing, measurements of bacterial production and chemical analyses of organic matter. The results revealed that the patchy distribution of productive coastal polynyas and less productive, mostly ice-covered sites was the major driver of the spatial changes in the taxonomic composition and activity of bacterioplankton. Gradients in organic matter availability induced by phytoplankton blooms were reflected in the concentrations and composition of dissolved carbohydrates and proteins. Bacterial production at bloom stations was, on average, 2.7 times higher than at less productive sites. Abundant bloom-responsive lineages were predominately affiliated with ubiquitous marine taxa, including Polaribacter, Yoonia-Loktanella, Sulfitobacter, the SAR92 clade, and Ulvibacter, suggesting a widespread genetic potential for adaptation to sub-zero seawater temperatures. A co-occurrence network analysis showed that dominant taxa at stations with low phytoplankton productivity were highly connected, indicating beneficial interactions. Overall, our study demonstrates that heterotrophic bacterial communities along Weddell Sea ice shelves were primarily constrained by the availability of labile organic matter rather than low seawater temperature.

Quantification of microcystin production and biodegradation rates in the western basin of Lake Erie.

Cyanobacterial biomass forecasts currently cannot predict the concentrations of microcystin, one of the most ubiquitous cyanotoxins that threaten human and wildlife health globally. Mechanistic insights into how microcystin production and biodegradation by heterotrophic bacteria change spatially and throughout the bloom season can aid in toxin concentration forecasts. We quantified microcystin production and biodegradation during two growth seasons in two western Lake Erie sites with different physicochemical properties commonly plagued by summer Microcystis blooms. Microcystin production rates were greater with elevated nutrients than under ambient conditions and were highest nearshore during the initial phases of the bloom, and production rates were lower in later bloom phases. We examined biodegradation rates of the most common and toxic microcystin by adding extracellular stable isotope‐labeled microcystin‐LR (1 μg L−1), which remained stable in the abiotic treatment (without bacteria) with minimal adsorption onto sediment, but strongly decreased in all unaltered biotic treatments, suggesting biodegradation. Greatest biodegradation rates (highest of −8.76 d−1, equivalent to the removal of 99.98% in 18 h) were observed during peak bloom conditions, while lower rates were observed with lower cyanobacteria biomass. Cell‐specific nitrogen incorporation from microcystin‐LR by nanoscale imaging mass spectrometry showed that a small percentage of the heterotrophic bacterial community actively degraded microcystin‐LR. Microcystin production and biodegradation rates, combined with the microcystin incorporation by single cells, suggest that microcystin predictive models could be improved by incorporating toxin production and biodegradation rates, which are influenced by cyanobacterial bloom stage (early vs. late bloom), nutrient availability, and bacterial community composition.

Dynamics of the Galionella spp. and Leptothrix spp. Communities of Polluted Mine Drainage Water in Slovinky and Markušovce (Slovakia)

Tailings ponds Slovinky and Markušovce (Slovakia) belong to the group of high-risk areas threatening human health and the environment due to the high concentrations of potentially toxic elements. The aim of this study was to identify iron bacteria living in these extreme environments and to assess the impact of selected physicochemical parameters of drainage water, flowing from tailings ponds, on the dynamics of their population. The material deposited on the Slovinky and Markušovce tailings pond showed a circumneutral pH. The values of electrical conductivity and total dissolved solids were significantly higher in drainage water in Slovinky compared to Markušovce. The concentration of total iron was notably higher in drainage water in Markušovce than in Slovinky. Direct microscopic observations showed the presence of iron-oxidizing bacteria as Gallionella spp. and Leptothix spp. exhibiting significant seasonal changes in their prevalence. The differences in the environmental characteristics of drainage waters did not affect the dynamics of iron-oxidizing bacteria populations, but cultivable heterotrophic bacterial community showed significantly lower abundance in Markušovce drainage water. The findings contribute to the understanding of bacterial diversity in neutral mine drainage waters and demonstrate an important role of environmental factors in shaping the microbial population in mine environments.

Fostering bacterial growth in BFT aquaculture tanks by early Nile tilapia stocking

The current study aimed at fostering bacterial growth in BFT aquaculture tanks by early Nile tilapia stocking. Control tanks had no tilapia but received daily applications of dry molasses (NT+) or had tilapia but no C:N ratio adjustment (T-). Experimental tanks had tilapia and received daily application of molasses to adjust the C:N ratio of water to 15:1 (T+). The development of bioflocs in NT+ was insignificant as demonstrated by low levels of settleable solids (SS) and total suspended solids (TSS). Total ammonia nitrogen (TAN) was significantly higher in NT+ than in T+. In the C:N-ratio adjusted tanks, the presence of fish shortened the control of TAN in several days. As nitrite declined in T+, it increased in NT+. The final concentrations of TSS in T+, T- and NT+ were 236 ± 29 mg L-1, 100 ± 32 mg L-1, and 40 ± 22 mg L-1, respectively (p &lt; 0.05). It can be concluded that stable nitrifying and heterotrophic bacterial communities could be attained in BFT aquaculture tanks, before the end of the 4th week of culture, if the bacterial growth is fostered by early Nile tilapia stocking.

The relationship between two Synechococcus strains and heterotrophic bacterial communities and its associated carbon flow

Synechococcus accounts for a considerable proportion of oceanic carbon fixation and has close relation with heterotrophic bacteria at sub-micrometre scales. However, the relationship between Synechococcus and heterotrophic bacteria and their impacts on oceanic carbon flow is not well understood. Here, we separately co-cultured the heterotrophic bacterial community with two different axenic Synechococcus strains, i.e. Synechococcus sp. PCC7002 and Synechococcus sp. CCMP1334. The dissolved organic carbon (DOC) released by Synechococcus promoted the rapid growth of heterotrophic bacteria. Due in part to the slight differences in the Synechococcus-derived DOC composition, the starting heterotrophic bacterial community was reshaped by the two Synechococcus strains into significantly divergent community structures, suggesting that different heterotrophic bacterial communities may gather around different Synechococcus strains and interact with each other in the oceans. Interestingly, the two Synechococcus strains also released some very stable humic-like DOC components that resisted use by heterotrophic bacteria and were gradually accumulated in seawater, implying that in addition to photosynthetic carbon fixation, Synechococcus may also play an important role in long-term ocean carbon sequestration by producing relatively recalcitrant DOC. Moreover, the interactions of Synechococcus and the heterotrophic bacterial communities could increase aggregate formation and particle sinking, which can likely enhance the contribution of Synechococcus to the magnitude of the sinking biological carbon pump in the oceans.

Molecular Basis for Substrate Recognition and Catalysis by a Marine Bacterial Laminarinase.

Laminarin is an abundant algal polysaccharide that serves as carbon storage and fuel to meet the nutrition demands of heterotrophic microbes. Laminarin depolymerization catalyzed by microbial extracellular enzymes initiates remineralization, a key process in ocean biogeochemical cycles. Here, we described a glycoside hydrolase 16 (GH16) family laminarinase from a marine alga-associated Flavobacterium at the biochemical and structural levels. We found that the endolytic enzyme cleaved laminarin with a preference for β-1,3-glycoside linkages and showed transglycosylation activity across a broad range of acceptors. We also solved and compared high-resolution crystal structures of laminarinase in the apo form and in complex with β-1,3-tetrasaccharides, revealing an expanded catalytic cleft formed following substrate binding. Moreover, structure and mutagenesis studies identified multiple specific contacts between the enzyme and glucosyl residues essential for the substrate specificity for β-1,3-glucan. These results provide novel insights into the structural requirements for substrate binding and catalysis of GH16 family laminarinase, enriching our understanding of bacterial utilization of algal laminarin.IMPORTANCE Heterotrophic bacterial communities are key players in marine biogeochemical cycling due to their ability to remineralize organic carbon. Processing of complex organic matter requires heterotrophic bacteria to produce extracellular enzymes with precise specificity to depolymerize substrates to sizes sufficiently small for uptake. Thus, extracellular enzymatic hydrolysis initiates microbe-driven heterotrophic carbon cycling. In this study, based on biochemical and structural analyses, we revealed the depolymerization mechanism of β-1,3-glucan, a carbon reserve in algae, by laminarinase from an alga-associated marine Flavobacterium The findings provide new insights into the substrate recognition and catalysis of bacterial laminarinase and promote a better understanding of how extracellular enzymes are involved in organic matter cycling.

Net Community Production, Dissolved Organic Carbon Accumulation, and Vertical Export in the Western North Atlantic

The annual North Atlantic phytoplankton bloom represents a hot spot of biological activity during which a significant fraction of net community production (NCP) can be partitioned into dissolved organic carbon (DOC). The fraction of seasonal NCP that is not respired by the heterotrophic bacterial community and accumulates as seasonal surplus DOC (∆DOC) in the surface layer represents DOC export to the upper mesopelagic zone, and in the North Atlantic this is facilitated by winter convective mixing that can extend to depths >400 m. However, estimates of ∆DOC and vertical DOC export for the western North Atlantic remain ill-constrained and the influence of phytoplankton community structure on the partitioning of seasonal NCP as ∆DOC is unresolved. Here, we couple hydrographic properties from autonomous in situ sensors (ARGO floats) with biogeochemical data from two meridional ship transects in the late spring (~ 44 – 56˚N along ~ -41˚W) and early autumn (~ 42 – 53˚N along ~ -41˚W) as part of the North Atlantic Aerosols and Marine Ecosystems Study (NAAMES). We estimate that 4 – 35% of seasonal NCP is partitioned as ∆DOC and that annual vertical DOC export ranges between 0.34 – 1.15 mol C m-2 in the temperate and subpolar North Atlantic. Two lines of evidence reveal that non-siliceous picophytoplankton, like Prochlorococcus, are indicator species of the conditions that control the accumulation of DOC and the partitioning of NCP as ∆DOC.

Diversity of Metal-Resistant and Tensoactive-Producing Culturable Heterotrophic Bacteria Isolated from a Copper Mine in Brazilian Amazonia

Bacterial extracellular polymeric substances (EPSs) present diverse properties of biotechnological interest, such as surface modification, metal adsorption and hydrophobic substances solubilization through surface tension reduction. Thus, there is a growing demand for new producing strains and structurally variable biomolecules with different properties. One approach for scanning this biodiversity consists of exploring environments under selective pressures. The aim of this study was to evaluate the composition of culturable heterotrophic bacterial communities from five different sites from a copper mine in the Amazon biome by an enrichment technique to obtain metal resistant bacteria (lead, arsenic, cadmium, copper and zinc) capable of producing EPSs. The bacterial densities at the sites varied from 2.42 × 103 to 1.34 × 108 NMP mL−1 and the 77 bacterial isolates obtained were classified in four divisions, β-Proteobacteria (16.88%), γ-Proteobacteria (7.29%), Firmicutes (61%) and Actinobacteria (12.98%). Bacillus, Alcaligenes, and Lysinibacillus were the most dominant among the 16 observed genera, but the relative frequency of each varied according to the sample and the metal used in the enrichment culture. 58% of the bacterial strains (45) could produce EPSs. From these, 33 strains showed emulsifying activity (E24), and 9 of them reached values higher than 49%. Only Actinomyces viscosus E3.Pb5 and Bacillus subtilis group E3.As2 reduced the medium surface tension to values lower than 35 mN m−1. It was possible to confirm the high presence of bacteria capable of producing EPSs with tensoactive properties in Amazon copper mines and the evolutionary pressure exerted by the heavy metals during enrichment. These molecules can be tested as an alternative for use in processes that involve the removal of metals, such as the bioremediation of contaminated environments.

Short-term changes in polysaccharide utilization mechanisms of marine bacterioplankton during a spring phytoplankton bloom.

Spring phytoplankton blooms in temperate environments contribute disproportionately to global marine productivity. Bloom-derived organic matter, much of it occurring as polysaccharides, fuels biogeochemical cycles driven by interacting autotrophic and heterotrophic communities. We tracked changes in the mode of polysaccharide utilization by heterotrophic bacteria during the course of a diatom-dominated bloom in the German Bight, North Sea. Polysaccharides can be taken up in a 'selfish' mode, where initial hydrolysis is coupled to transport into the periplasm, such that little to no low-molecular weight (LMW) products are externally released to the environment. Alternatively, polysaccharides hydrolyzed by cell-surface attached or free extracellular enzymes (external hydrolysis) yield LMW products available to the wider bacterioplankton community. In the early bloom phase, selfish activity was accompanied by low extracellular hydrolysis rates of a few polysaccharides. As the bloom progressed, selfish uptake increased markedly, and external hydrolysis rates increased, but only for a limited range of substrates. The late bloom phase was characterized by high external hydrolysis rates of a broad range of polysaccharides and reduced selfish uptake of polysaccharides, except for laminarin. Substrate utilization mode is related both to substrate structural complexity and to the bloom-stage dependent composition of the heterotrophic bacterial community.