Bacterioplankton Community Research Articles

Stronger biogeographical pattern of bacterioplankton communities than biofilm communities along a riverine ecosystem: a local scale study of the Kaidu river in the arid and semi-arid northwest of China

Although the biogeographical pattern and mechanisms underlying microbial assembly have been well-explored in lentic ecosystems, the relevant scenarios in lotic ecosystems remain poorly understood. By sequencing the bacterial communities in bacterioplankton and biofilm, our study detected their distance-decay relationship (DDR), and the balance between deterministic and stochastic processes, along the Kaidu river in an arid and semi-arid region of northwest China. Our results revealed that bacterioplankton and biofilm had significantly contrasting community structures. The bacterioplankton communities showed a gradually decreasing trend in alpha-diversity from the headwater to the river mouth, contrasting with the alpha-diversity of biofilm communities which was constant along the river length. Both bacterioplankton and biofilm showed significant DDRs along the 500-km river corridor with the slope of the bacterioplankton DDR being steeper than that of the biofilm DDR, which implies a stronger biogeography of bacterioplankton than biofilm. Relative to biofilm communities, the species interactions formed a denser and more complex network in the bacterioplankton communities than in the biofilm communities. Our results also revealed that there was a transition of community assembly from deterministic to stochastic processes upstream to downstream, although both the bacterioplankton and biofilm communities were mainly regulated by deterministic processes within the entire river. All these empirical results expand our knowledge of microbial ecology in an arid and semi-arid lotic ecosystem.

Higher Contribution of Generalists Than Specialists to the Bacterial Biogeography Across Lakes in Northern China

ABSTRACTAimGiven that microbial communities normally comprise generalist and specialist species, there have been limited efforts to estimate the contribution of these sub‐communities to bacterial biogeography regarding ecological assembly processes and nestedness structure. To resolve this gap, we studied the spatial distribution of bacterioplankton communities and their generalist and specialist sub‐communities, as well as the underlying assembly processes.LocationSix lakes span three climate zones in northern China.Time PeriodSeptember 2021.MethodsBy separately analysing the generalist and specialist sub‐communities from the whole communities, we investigated the relationships between sub‐communities and the entire communities in terms of distance‐decay pattern, nestedness, and assembly processes. As such, we assessed the contribution of generalist and specialist sub‐communities to the biogeographic patterns of the whole communities.Major Taxa StudiesBacterial community.ResultsGeneralist sub‐communities were more diverse but less abundant than specialist sub‐communities. In line with the whole communities, both types of sub‐communities exhibited distance‐decay relationships at the regional scale, with the slope of specialists being steeper than that of generalists. Additionally, generalist sub‐communities and whole communities also exhibited similar nestedness patterns, in which assemblages from saline water were the subset of those from freshwater. In terms of assembly processes, generalist sub‐communities and whole communities were strongly regulated by homogeneous selection, whereas specialist sub‐communities were mainly shaped by dispersal limitation. More importantly, there was a transition from stochastic to deterministic assembly processes for generalist sub‐communities and whole communities and generalist sub‐communities with increasing total dissolved solids.Main ConclusionsRelative to the specialists, the assembly processes and nestedness pattern were more altered if the generalists were absent, which implies the higher contribution of generalist sub‐communities on the biogeography of whole communities at the regional scale.

Coral high molecular weight carbohydrates support opportunistic microbes in bacterioplankton from an algae-dominated reef.

Dissolved organic matter (DOM) released by benthic primary producers fuels coral reef food webs. Anthropogenic stressors cause shifts from coral to algae dominance on many reefs, and resulting alterations in the DOM pool can promote opportunistic microbes and potential coral pathogens in reef water. To better understand these DOM-induced effects on bacterioplankton communities, we compared the carbohydrate composition of coral- and macroalgae-DOM and analyzed the response of bacterioplankton from an algae-dominated reef to these DOM types. In line with the proposed microbialization of reefs, coral-DOM was efficiently utilized, promoting energy transfer to higher trophic levels, whereas macroalgae-DOM likely stimulated microbial respiration over biomass production. Contrary to earlier findings, coral- and not algal-DOM selected for opportunistic microbial taxa, indicating that a change in the prevalent DOM composition, and not DOM type, may promote the rise of opportunistic microbes. Presented results may also apply to other coastal marine ecosystems undergoing benthic community shifts.

Impact of Top-Down Regulation on the Growth Efficiency of Freshwater Bacterioplankton

To investigate the hypothesis of top-down control by viruses and heterotrophic nanoflagellates on bacterial-mediated carbon fluxes in freshwater systems, a year-long study (2023–2024) was conducted in the pelagic zone of Lake Saint-Gervais (France). The variability in BGE (9.9% to 45.5%) was attributed to the decoupling of production and respiration, providing bacterioplankton communities with a competitive advantage in adapting to fluctuating environmental disturbances in freshwater systems. The high nucleic acid (HNA) bacterial community, the active fraction, contributed the most to bacterial production and was linked to BGE estimates. Weak bottom-up controls (nutrient concentrations and stoichiometry) on BGE suggested a stronger role for mortality forces. Among viral subgroups (VLP1–VLP4) identified via flow cytometry, the dominant low-fluorescence DNA VLP1 subgroup (range = 0.7 to 3.1 × 108 VLP mL−1) accounting for the majority of viral production was closely linked to the HNA population. Both top-down forces exerted antagonistic effects on BGE at the community level. The preferential lysis and grazing of the susceptible HNA population, which stimulated bacterial community respiration more than production in the non-target population, resulted in reduced BGE. These results underscore the key role of top-down processes in shaping carbon flux through bacterioplankton in this freshwater system.

Tidal levels significantly change bacterial community composition in a tropical estuary during the dry season

AbstractEstuaries are usually characterized by strong spatial and temporal variability in water physicochemical conditions and are often largely affected by human activities. One important source of variability is caused by tides that can swiftly alter not only physicochemical conditions but also the abundance and composition of the biota. The effect of the diurnal tidal cycle on microbial community composition during different seasons remains uncertain, although this knowledge underlies having effective monitoring programs for water quality and potential identification of health risk conditions. In this study, we assessed the bacterioplankton community composition and diversity across four tidal water levels in a tropical estuary characterized by a mixed semidiurnal tide regime (i.e., two high and two low tides of varying amplitudes) during both dry and wet seasons. The bacterial community composition varied significantly among the four tidal levels, but only during the dry season, when the influence of the seawater intrusion was largest. Bacterial indicators’ taxa identified using the Indicator Value Index were found within Cyanobacteria, Actinobacteriota, Bacteroidota, and Proteobacteria. The indicator taxon Cyanobium sp. had a prominent presence across multiple tidal levels. The main predicted phenotypes of the bacterial communities were associated with potential pathogenicity, gram-negative, and biofilm formation traits. While there were no marked predicted phenotypic differences between seasons, pathogenic and gram-negative traits were more prevalent in the dry season, while biofilm formation traits dominated in the wet season. Overall, our findings underscore the intricate relationship between river hydrodynamics and bacterial composition variability and hint a significant human impact on the water quality of the Bangpakong River.

Environmental factors that regulate Vibrio spp. abundance and community structure in tropical waters

Vibrio spp. is a group of heterotrophic bacteria that are ubiquitous in marine habitats, with various ecological and clinical importance. This study investigated the environmental factors that regulate Vibrio spp. dynamics in various tropical marine habitats, including nearshore (an estuary and a coastal beach) and offshore transects located northwest and southeast of Peninsular Malaysia, while focusing on the distribution of attached and free-living Vibrio spp., population growth, and community composition. The results showed that > 85% of the Vibrio spp. in nearshore waters occurred in attached form and correlated positively to total suspended solids (TSS) and Chlorophyll a (Chl a) concentrations. On the other hand, Vibrio spp. growth rates were positively correlated to dissolved organic carbon (DOC) concentrations, but negatively correlated to total bacterial counts, likely due to resource competition. In addition, high-throughput sequencing of 16S rRNA V3-V4 region showed that Vibrio spp. in these tropical waters contributed < 1 − 18% of the whole bacterioplankton community, and the six major Vibrio spp. taxa were V. alginolyticus group, V. brasiliensis, V. caribbeanicus, V. hepatarius group, V. splendidus group and V. thalassae. db-RDA (cumulative variance explicated = 93.53%) further revealed the influence of TSS, DOC, and dissolved organic nitrogen (DON) to the Vibrio spp. community profiles. The study highlighted the importance of suspended solids (TSS and Chl a) and dissolved organic nutrients (DOC and DON) towards Vibrio spp. dynamics in tropical marine waters.

Seasonal dynamics of environmental heterogeneity augment microbial interactions by regulating community structure in different trophic lakes

Understanding how environmental heterogeneity drives microbial communities in lakes is essential for developing effective strategies to manage and restore aquatic ecosystems. However, the mechanisms by which environmental heterogeneity influences microbial community structure, network patterns, and interactions remain largely unexplored. To bridge this gap, we collected 84 water samples from four typical lakes in China (Fuxian, Tianmu, Taihu, and Xingyun) representing a range of trophic levels, across wet and dry seasons. We assessed environmental heterogeneity using 14 water quality parameters, analyzed community structure with Jaccard and Bray-Curtis dissimilarity indices, and developed a comprehensive index to elucidate microbial network complexity. Our study reveals three key findings: (1) Environmental heterogeneity was significantly greater in dry season compared to wet season across all lakes (P < 0.05). (2) Increased environmental heterogeneity led to higher bacterioplankton community dissimilarity, with greater β-diversity observed in dry season (P < 0.05). (3) Shifts in community structure due to increased environmental heterogeneity further enhanced microbial interactions, as evidenced by more complex and interconnected co-occurrence networks in the dry season. In summary, our study demonstrates that environmental heterogeneity significantly impacts bacterioplankton community structure and subsequently enhances microbial interactions. These findings underscore the importance of considering environmental heterogeneity in lake ecosystem management, as it plays a crucial role in regulating microbial community dynamics and interactions.

How Big Is Big? The Effective Population Size of Marine Bacteria.

Genome-reduced bacteria constitute most of the cells in surface-ocean bacterioplankton communities. Their extremely large census population sizes (N c) have been unfoundedly translated to huge effective population sizes (N e)-the size of an ideal population carrying as much neutral genetic diversity as the actual population. As N e scales inversely with the strength of genetic drift, constraining the magnitude of N e is key to evaluating whether natural selection can overcome the power of genetic drift to drive evolutionary events. Determining the N e of extant species requires measuring the genomic mutation rate, a challenging step for most genome-reduced bacterioplankton lineages. Results for genome-reduced Prochlorococcus and CHUG are surprising-their N e values are an order of magnitude lower than those of less abundant lineages carrying large genomes, such as Ruegeria and Vibrio. As bacterioplankton genome reduction commonly occurred in the distant past, appreciating their population genetic mechanisms requires constraining their ancient N e values by other methods.

Ecological filtering drives rapid spatiotemporal dynamics in fish skin microbiomes.

Skin microbiomes provide vital functions, yet knowledge about the drivers and processes structuring their species assemblages is limited-especially for non-model organisms. In this study, fish skin microbiome was assessed by high throughput sequencing of amplicon sequence variants from metabarcoding of V3-V4 regions in the 16S rRNA gene on fish hosts subjected to the following experimental manipulations: (i) translocation between fresh and brackish water habitats to investigate the role of environment; (ii) treatment with an antibacterial disinfectant to reboot the microbiome and investigate community assembly and priority effects; and (iii) maintained alone or in pairs to study the role of social environment and inter-host dispersal of microbes. The results revealed that fish skin microbiomes harbour a highly dynamic microbial composition that was distinct from bacterioplankton communities in the ambient water. Microbiome composition first diverged as an effect of translocation to either the brackish or freshwater habitat. When the freshwater individuals were translocated back to brackish water, their microbiome composition converged towards the fish microbiomes in the brackish habitat. In summary, external environmental conditions and individual-specific factors jointly determined the community composition dynamics, whereas inter-host dispersal had negligible effects. The dynamics of the microbiome composition was seemingly non-affected by reboot treatment, pointing towards high resilience to disturbance. The results emphasised the role of inter-individual variability for the unexplained variation found in many host-microbiome systems, although the mechanistic underpinnings remain to be identified.

Temperature-driven shifts in bacterioplankton biodiversity: Implications for cold-preferred species in warming Tibetan proglacial lakes

Recent climate warming and associated glacier retreat have dramatically changed the environmental conditions and microbial inhabitants of proglacial lakes. However, our understanding of the effects of climate warming and glacial influence on microbial biodiversity in these lakes remain relatively limited. Here, we studied bacterioplankton communities in 22 proglacial lakes on the Tibetan Plateau, spanning a range of nearly 7 °C in mean annual temperature (MAT), and examined the effects of climate and glaciers on their biodiversity by a space-to-time substitution. MAT emerged as the primary environmental driver of bacterioplankton biodiversity compared to glacial influence, increasing species richness and decreasing β-diversity. We identified 576 low-MAT (cold-preferred) species and 2,088 high-MAT (warm-preferred) species, and found that low-MAT species are less environmentally adapted, with their numbers declining as temperature increased. These results advance our understanding of temperature-driven bacterioplankton dynamics by disentangling the contrasting responses and adaptations of cold-preferred and warm-preferred species. Our findings highlight the vulnerability of cold-specialist taxa and the potential biodiversity losses associated with climate warming in the rapidly changing proglacial lakes.

Consistent responses of the shrimp Litopenaeus vannamei gut microbiota to Enterocytozoon hepatopenaei infection across spatially distant farms

The gut microbiota of aquatic animals is supposed to be sourced from rearing water. However, bacterioplankton communities exhibit a biogeographic pattern, raising the question whether the gut microbiota respond consistently to shrimp health status across spatially distant farms. Here, we collected shrimp Litopenaeus vannamei samples infected with Enterocytozoon hepatopenaei (EHP) from six geographically distant farms with varying local conditions. The gut microbiota of healthy shrimp differed significantly across aquaculture locations, while EHP infection effect was also detectable at each location. Therefore, we ruled out the location effect by removing taxa that featured location. After this optimization, we identified 23 EHP-discriminatory taxa that accurately diagnosed EHP infection, achieving an overall accuracy of 90.5%. Structural equation model revealed that water pH and NO3− levels were the governing factors for the bacterioplankton community. However, the shrimp gut microbiota was not strongly affected by the bacterioplankton community in their rearing water. EHP infection consistently increased deterministic processes and destabilized the biotic network in the shrimp gut microbiota. Collectively, our findings provide evidence that EHP infection causes consistent changes, e.g., altered structure, increased determinism, and destabilized network, in the gut microbiota across spatially distant farms. In particular, we established a diagnosis model for diagnosing EHP infection that is independent of aquaculture location.

Seasonality of amino acid enantiomers and microbial communities at MOLA time series in the NW Mediterranean Sea

Seasonality in light, temperature, and nutrient availability are well-known to regulate phytoplankton blooms and the bacterioplankton community. During the spring bloom, phytoplankton release biomolecules as part of the dissolved organic matter (DOM) pool exploited by the bacterioplankton. Here, we investigated the seasonal variability of phytoplankton biomass, enantiomers of dissolved hydrolyzable amino acids (DHAA), bacterioplankton abundances and community composition at the Microbial Observatory Laboratory Arago (MOLA) in the NW Mediterranean Sea from 2019 to 2021. Phytoplankton biomass estimated from pigment biomarkers suggests a spring bloom succession from cryptophytes, haptophytes, and prasinophytes in March to diatoms in April. The spring bloom coincided with a 50% increase in L-enantiomers of DHAA and an increase in bacterial abundance. After the spring bloom, elevated concentrations of D-enantiomers of DHAA and gamma-aminobutyric acid suggest bacterial processing of labile biomolecules contributed to the seasonal accumulation of dissolved organic carbon (DOC). Linking organic molecules with the free-living bacterioplankton community showed a seasonal succession of niches and substrate regimes. The parallel analysis of DOM and bacterioplankton community provides an important baseline for bacteria-substrate relationships over the seasonal cycle in the northwestern Mediterranean Sea.

Dynamic population modeling of bacterioplankton community response to gelatinous marine zooplankton bloom collapse and its impact on marine nutrient balance

The diverse microbial community in the ocean, encompassing various metabolic types, interacts with the wide array of compounds in the dissolved organic matter (DOM) pool, thereby influencing the ocean’s biogeochemical state and, consequently, the global climate. Our understanding of the interactions between specific DOM constituents and microbial consortia remains limited, necessitating further refinement to achieve a mechanistic comprehension of the relationship between the DOM field and the microbial metabolic network. Attaining this level of understanding is crucial for accurately predicting the marine ecosystem’s response to natural and anthropogenic perturbations. To address this gap, we developed a bacterial population model based on the von Foerster equation. This model aims to describe the complex microbial-mediated degradation of gelatinous zooplankton (hereinafter ‘jellyfish’) detritus, as an important, but largely overlooked source of DOM in the ocean. By considering microbial growth and decay, as well as DOM uptake, and nutrient release, the model is able to describe the microbial community’s life cycle, and the biochemical transformations of the jellyfish-derived organic matter. We fitted the model to results of laboratory microcosm experiments conducted to simulate scenarios experienced by ambient microbiomes during decay of two different jellyfish species in the northern Adriatic Sea. By interpreting the fitted parameters, we highlight the differences in the microbial response to different jellyfish species, namely how these affect the microbial community composition and the release of nutrients. This model has been specifically designed for integration with ocean circulation models to create a comprehensive physical-biogeochemical ocean model. Such an extended model can be utilized for multi-scale simulations to assess the system’s response to jellyfish and jellyfish-derived organic matter. Given that jellyfish blooms may become more prevalent under future ocean scenarios, this modeling approach is essential for understanding their potential impact on marine ecosystems.

Vertical Distribution Characteristics and Driving Factors of Bacterioplankton and Nitrogen Phosphorus Cycle Genes in Danjiangkou Reservoir

Danjiangkou Reservoir is a critical water source for the South-to-North Water Diversion Project, which harbors a diverse bacterioplankton community with varying depths, and the understanding of its nitrogen and phosphorus cycle and associated driving factors remains limited. In this study, we selected five ecological sites within Danjiangkou Reservoir and conducted metagenomics analysis to investigate the vertical distribution of bacterioplankton communities in the surface, middle, and bottom layers. Furthermore, we analyzed and predicted the function of nitrogen and phosphorus cycles, along with their driving factors. Our findings revealed the dominance of Proteobacteria, Actinobacteria, and Planctomycetes in the Danjiangkou Reservoir. Significant differences were observed in the structure of bacterioplankton communities across different depths, with temperature （T）, oxidation-reduction potential （ORP）, dissolved oxygen （DO）, and Chla identified as primary factors influencing the bacterioplankton composition. Analysis of nitrogen cycle functional genes identified 39 genes, including gltB, glnA, gltD, gdhA, NRT, etc., which were involved in seven main pathways, encompassing nitrogen fixation, nitrification, denitrification, and dissimilatory nitrate reduction. Phosphorus cycle function gene analysis identified 54 genes, including pstS, ppx-gppA, glpQ, ppk1, etc., primarily participating in six main pathways, including organic P mineralization, inorganic P solubilization, and regulatory. Cluster analysis indicated that different depths were significant factors influencing the composition and abundance of nitrogen and phosphorus cycle functional genes. The composition and abundance of nitrogen and phosphorus cycle functional genes in the surface and bottom layers differed and were generally higher than those in the middle layer. Deinococcus, Hydrogenophaga, Limnohabitans, Clavibacter, and others were identified as key species involved in the nitrogen and phosphorus cycle. Additionally, we found significant correlations between nitrogen and phosphorus cycle functional genes and environmental factors such as DO, pH, T, total dissolved solids （TDS）, electrical conductivity （EC）, and Chla. Furthermore, the content of these environmental factors exhibited depth-related changes in the Danjiangkou Reservoir, resulting in a distinct vertical distribution pattern of bacterioplankton nitrogen and phosphorus cycle functional genes. Overall, this study sheds light on the composition, function, and influencing factors of bacterioplankton communities across different layers of Danjiangkou Reservoir, offering valuable insights for the ecological function and diversity protection of bacterioplankton in this crucial reservoir ecosystem.

Exploring the environmental influences and community assembly processes of bacterioplankton in a subtropical coastal system: Insights from the Beibu Gulf in China

Due to rapid urbanization, the Beibu Gulf, a semi-closed gulf in the northwestern South China Sea, faces escalating ecological and environmental threats. Understanding the assembly mechanisms and driving factors of bacterioplankton in the Beibu Gulf is crucial for preserving its ecological functions and services. In the present study, we investigated the spatiotemporal dynamics of bacterioplankton communities and their assembly mechanisms in the Beibu Gulf based on the high-throughput sequencing of the bacterial 16 S rRNA gene. Results showed significantly higher bacterioplankton diversity during the wet season compared to the dry season. Additionally, distinct seasonal variations in bacterioplankton composition were observed, characterized by an increase in Cyanobacteria and Thermoplasmatota and a decrease in Proteobacteria and Bacteroidota during the wet season. Null model analysis revealed that stochastic processes governed bacterioplankton community assembly in the Beibu Gulf, with drift and homogenizing dispersal dominating during the dry and wet seasons, respectively. Enhanced deterministic assembly of bacterioplankton was also observed during the wet season. Redundancy and random forest model analyses identified the physical properties (e.g., temperature) and nutrient content (e.g., nitrate) of water as primary environmental drivers influencing bacterioplankton dynamics. Moreover, variation partitioning and distance-decay of similarity revealed that environmental filtering played a significant role in shaping bacterioplankton variations in this rapidly developed coastal ecosystem. These findings advance our understanding of bacterioplankton assembly in coastal ecosystems and establish a theoretical basis for effective ecological health management amidst ongoing global changes.

Integrated Rice–Fish Culture Alters the Bacterioplankton Community and Its Assembly Processes

The rice–fish co-culture is an important model of carp farming in China; however, research on the dynamics and assembly of water bacterial communities in this system remains limited. Therefore, this study aimed to explore the dynamics and assembly of bacterial communities, as well as their correlation with environmental factors in paddy water. For these purposes, this study was divided into two groups: a rice–carp co-culture (WRC) group and a rice monoculture (WRM) group, with 20 rice fields in each group. After 60 days of farming, the concentrations of NH4+-N, NO2−-N, TN, and PO43− were significantly higher in the WRC group than those in the WRM group. Alpha diversity analysis showed that the Shannon index in the WRC group was significantly decreased compared with the WRM group. At the phylum level, the relative abundance of Actinobacteria significantly increased, while the relative abundance of Proteobacteria and Bacteroidetes significantly decreased in the paddy water of the WRC group. The neutral community model (NCM) indicated that a random process played a dominant role in the construction of bacterial communities in the two groups, and common carp cultivation increased migration rates, thereby affecting community assembly. The co-occurrence network displayed that common carp cultivation led to looser interactions between bacterial communities. In addition, the contents of nutrients significantly affected the abundance of bacteria in paddy water. In summary, carp cultivation decreased the diversity of bacteria and changed the relative abundance of dominant bacteria, thereby affecting the stability and assembly of bacterial communities.

Seasonal and anthropogenic influences on bacterioplankton communities: ecological impacts in the coastal waters of Qinhuangdao, Northern China.

Marine bacterioplankton play a crucial role in the cycling of carbon, nitrogen, and phosphorus in coastal waters. And the impact of environmental factors on bacterial community structure and ecological functions is a dynamic ongoing process. To systematically assess the relationship between environmental changes and bacterioplankton communities, this study delved into the spatiotemporal distribution and predicted metabolic characteristics of bacterioplankton communities at two estuarine beaches in Northern China. Coastal water samples were collected regularly in spring, summer, and autumn, and were analyzed in combination with environmental parameters and bacterioplankton community. Results indicated significant seasonal variations in bacterioplankton communities as Bacteroidetes and Actinobacteria were enriched in spring, Cyanobacteria proliferated in summer. While Pseudomonadota and microorganisms associated with organic matter decomposition prevailed in autumn, closely linked to seasonal variation of temperature, light and nutrients such as nitrogen and phosphorus. Particularly in summer, increased tourism activities and riverine inputs significantly raised nutrient levels, promoting the proliferation of specific photosynthetic microorganisms, potentially linked to the occurrence of phytoplankton blooms. Spearman correlation analysis further revealed significant correlations between bacterioplankton communities and environmental factors such as salinity, chlorophyll a, and total dissolved phosphorus (TDP). Additionally, the metabolic features of the spring bacterioplankton community were primarily characterized by enhanced activities in the prokaryotic carbon fixation pathways, reflecting rapid adaptation to increased light and temperature, as well as significant contributions to primary productivity. In summer, the bacterial communities were involved in enhanced glycolysis and biosynthetic pathways, reflecting high energy metabolism and responses to increased light and biomass. In autumn, microorganisms adapted to the accelerated decomposition of organic matter and the seasonal changes in environmental conditions through enhanced amino acid metabolism and material cycling pathways. These findings demonstrate that seasonal changes and human activities significantly influence the structure and function of bacterioplankton communities by altering nutrient dynamics and physical environmental conditions. This study provides important scientific insights into the marine biological responses under global change.

Determination of the Microorganisms’ Resistance to Antibiotics in the Bacterioplankton Community in the Akmola Region Lakes

Determination of the Microorganisms’ Resistance to Antibiotics in the Bacterioplankton Community in the Akmola Region Lakes

Description of a 'plankton filtration bias' in sequencing-based bacterial community analysis and of an Arduino microcontroller-based flowmeter device that can help to resolve it.

Diversity studies of aquatic picoplankton (bacterioplankton) communities using size-class filtration, DNA extraction, PCR and sequencing of phylogenetic markers, require a robust methodological pipeline, since biases have been demonstrated essentially at all levels, including DNA extraction, primer choice and PCR. Even different filtration volumes of the same plankton sample and, thus, different biomass loading of the filters, can distort the sequencing results. In this study, we designed an Arduino microcontroller-based flowmeter that records the decrease of initial (maximal) flowrate as proxy for increasing biomass loading and clogging of filters during plankton filtration. The device was tested using freshwater plankton of Lake Constance, and total DNA was extracted and an 16S rDNA amplicon was sequenced. We confirmed that different filtration volumes used for the same water sample affect the sequencing results. Differences were visible in alpha and beta diversities and across all taxonomic ranks. Taxa most affected were typical freshwater Actinobacteria and Bacteroidetes, increasing up to 38% and decreasing up to 29% in relative abundance, respectively. In another experiment, a lake water sample was filtered undiluted and three-fold diluted, and each filtration was stopped once the flowrate had reduced to 50% of initial flowrate, hence, at the same degree of filter clogging. The three-fold diluted sample required three-fold filtration volumes, while equivalent amounts of total DNA were extracted and differences across all taxonomic ranks were not statistically significant compared to the undiluted controls. In conclusion, this work confirms a volume/biomass-dependent bacterioplankton filtration bias for sequencing-based community analyses and provides an improved procedure for controlling biomass loading during filtrations and recovery of equivalent amounts of DNA from samples independent of the plankton density. The application of the device can also avoid the distorting of sequencing results as caused by the plankton filtration bias.

Structure and composition of microbial communities in the water column from Southern Gulf of Mexico and detection of putative hydrocarbon-degrading microorganisms.

This study assessed the bacterioplankton community and its relationship with environmental variables, including total petroleum hydrocarbon (TPH) concentration, in the Yucatan shelf area of the Southern Gulf of Mexico. Beta diversity analyses based on 16S rRNA sequences indicated variations in the bacterioplankton community structure among sampling sites. PERMANOVA indicated that these variations could be mainly related to changes in depth (5 to 180 m), dissolved oxygen concentration (2.06 to 5.93 mg L-1), and chlorophyll-a concentration (0.184 to 7.65 mg m3). Moreover, SIMPER and one-way ANOVA analyses showed that the shifts in the relative abundances of Synechococcus and Prochlorococcus were related to changes in microbial community composition and chlorophyll-a values. Despite the low TPH content measured in the studied sites (0.01 to 0.86 μL L-1), putative hydrocarbon-degrading bacteria such as Alteromonas, Acinetobacter, Balneola, Erythrobacter, Oleibacter, Roseibacillus, and the MWH-UniP1 aquatic group were detected. The relatively high copy number of the alkB gene detected in the water column by qPCR and the enrichment of hydrocarbon-degrading bacteria obtained during lab crude oil tests exhibited the potential of bacterioplankton communities from the Yucatan shelf to respond to potential hydrocarbon impacts in this important area of the Gulf Mexico.