Microbial community successions and their dynamic functions during harmful cyanobacterial blooms in a freshwater lake

Authors

Hanyan Li, Mike Barber, Jingrang Lu, Ramesh Goel

The current study reports the community succession of different toxin and non-toxin producing cyanobacteria at different stages of cyanobacterial harmful algal blooms (CyanoHABs) and their connectivity with nitrogen and phosphorus cycles in a freshwater lake using an ecogenomics framework. Comprehensive high throughput DNA sequencing, water quality parameter measurements, and functional gene expressions over temporal and spatial scales were employed. Among the cyanobacterial community, the lake was initially dominated by Cyanobium during the months of May, June, and early July, and later primarily by Aphanizomenon and Dolichospermum depicting functional redundancy. Finally, Planktothrix appeared in late August and then the dominance switched to Planktothrix in September. Microcystis aeruginosa and Microcystis panniformis; two species responsible for cyanotoxin production, were also present in August and September, but in significantly smaller relative abundance. MC-LR (0.06–1.32 µg/L) and MC-RR (0.01–0.26 µg/L) were two major types of cyanotoxins detected. The presence of MC-LR and MC-RR were significantly correlated with the Microcystis-related genes (16SMic/mcyA/mcyG) and their expressions (r = 0.33 to 0.8, p < 0.05). The metabolic analyses further linked the presence of different cyanobacterial groups with distinct functions. The nitrogen metabolisms detected a relatively higher abundance of nitrite/nitrate reductase in early summer, indicating significant denitrification activity and the activation of N-fixation in the blooms dominated by Aphanizomenon/Dolichospermum (community richness) during nutrient-limited conditions. The phosphorus and carbohydrate metabolisms detected a trend to initiate a nutrient starvation alert and store nutrients from early summer, while utilizing the stored polyphosphate and carbohydrate (PPX and F6PPK) during the extreme ortho-P scarcity period, mostly in August or September. Specifically, the abundance of Aphanizomenon and Dolichospermum was positively correlated with the nitrogen-fixing nif gene and (p < 0.001) and the PPX enzyme for the stored polyphosphate utilization (r = 0.77, p < 0.001). Interestingly, the lake experienced a longer N-fixing period (2–3 months) before non-fixing cyanobacteria (Planktothrix) dominated the entire lake in late summer. The Provo Bay site, which is known to be nutrient-rich historically, had early episodes of filamentous cyanobacteria blooms compared to the rest of the lake.

Rapid shifts in methanotrophic bacterial communities mitigate methane emissions from a tropical hydropower reservoir and its downstream river

Authors

Paula C. J. Reis, Clara Ruiz-González, Sophie Crevecoeur, Cynthia Soued, Yves T. Prairie

Methane-oxidizing bacteria (MOB) present in the water column mitigate methane (CH₄) emissions from hydropower complexes to the atmosphere. By creating a discontinuity in rivers, dams cause large environmental variations, including in CH₄ and oxygen concentrations, between upstream, reservoir, and downstream segments. Although highest freshwater methanotrophic activity is often detected at low oxygen concentrations, CH₄ oxidation in well-oxygenated downstream rivers below dams has also been reported. Here we combined DNA and RNA high-throughput sequencing with microscopic enumeration (by CARD-FISH) and biogeochemical data to investigate the abundance, composition, and potential activity of MOB taxa from upstream to downstream waters in the tropical hydropower complex Batang Ai (Malaysia). High relative abundance of MOB (up to 61% in 16S rRNA sequences and 19% in cell counts) and enrichment of stable isotopic signatures of CH₄ (up to 0‰) were detected in the hypoxic hypolimnion of the reservoir and in the outflowing downstream river. MOB community shifts along the river-reservoir system reflected environmental sorting of taxa and an interrupted hydrologic connectivity in which downstream MOB communities resembled reservoir’s hypolimnetic communities but differed from upstream and surface reservoir communities. In downstream waters, CH₄ oxidation was accompanied by fast cell growth of particular MOB taxa. Our results suggest that rapid shifts in active MOB communities allow the mitigation of CH₄ emissions from different zones of hydropower complexes, including in quickly re-oxygenated rivers downstream of dams.

A novel cyanobacterial geosmin producer, revising GeoA distribution and dispersion patterns in Bacteria

Authors

Catarina Churro, Ana P. Semedo-Aguiar, Alexandra D. Silva, Jose B. Pereira-Leal & Ricardo B. Leite

Cyanobacteria are ubiquitous organisms with a relevant contribution to primary production in all range of habitats. Cyanobacteria are well known for their part in worldwide occurrence of aquatic blooms while producing a myriad of natural compounds, some with toxic potential, but others of high economical impact, as geosmin. We performed an environmental survey of cyanobacterial soil colonies to identify interesting metabolic pathways and adaptation strategies used by these microorganisms and isolated, sequenced and assembled the genome of a cyanobacterium that displayed a distinctive earthy/musty smell, typical of geosmin, confirmed by GC-MS analysis of the culture’s volatile extract. Morphological studies pointed to a new Oscillatoriales soil ecotype confirmed by phylogenetic analysis, which we named Microcoleus asticus sp. nov. Our studies of geosmin gene presence in Bacteria, revealed a scattered distribution among Cyanobacteria, Actinobacteria, Delta and Gammaproteobacteria, covering different niches. Careful analysis of the bacterial geosmin gene and gene tree suggests an ancient bacterial origin of the gene, that was probably successively lost in different time frames. The high sequence similarities in the cyanobacterial geosmin gene amidst freshwater and soil strains, reinforce the idea of an evolutionary history of geosmin, that is intimately connected to niche adaptation.

Temporal heterogeneity of microbial communities and metabolic activities during a natural algal bloom

Authors

Jin Zhou, Yong-min Lao, Jun-ting Song, Hui Jin, Jian-ming Zhu, Zhong-hua Cai

Elucidating the interactions between algae and associated microbial communities is critical for understanding the mechanisms that mediate the dynamic of harmful algal blooms (HABs) in marine environment. However, the microbial functional profiles and their biogeochemical potential in HABs process remains elusive, especially during a complete natural HAB cycle. Here, we used pyrosequencing and functional gene array (GeoChip) to investigate microbial community dynamics and metabolic potential during a natural dinoflagellate (Noctiluca scintillans) bloom. The results shown that bacterioplankton exhibited significant temporal heterogeneity over the course of the bloom stages. Microbial succession was co-driven by environmental parameters and biotic interactions. The functional analysis revealed significant variations in microbial metabolism during matter cycling. At bloom onset-stage, metabolic potential associated with iron oxidation and transport was elevated. Carbon fixation and degradation, denitrification, phosphorus acquisition, and sulfur transfer/oxidation were significantly enhanced at the plateau stage. During the decline and terminal stages, oxidative stress, lysis of compounds, and toxin degradation & protease synthesis increased. This work reveal phycosphere microorganisms can enhanced organic C decomposition capacity, altered N assimilation rate and S/P turnover efficiency, and balancing of the Fe budget during HAB process. The ecological linkage analysis has further shown that microbial composition and functional potential were significantly linked to algal blooms occurrence. It suggest that structural variability and functional plasticity of microbial communities influence HAB trajectory.

Formation of N-nitrosodimethylamine precursors through the microbiological metabolism of nitrogenous substrates in water

Authors

Er Bei, Xiao Li, Fuhua Wu, Shixiang Li, Xinsheng He, Yufang Wang, Yu Qiu, Yu Wang, Chengkun Wang, Jun Wang, Xiaojian Zhang, Chao Chen

N-nitrosodimethylamine (NDMA) as one emerging disinfection by-product has been investigated globally since 1990s. However, its main precursors are still unclear. We found that NDMA formation potential (NDMAFP) of various water samples increased firstly and then decreased gradually during incubation with microorganism. We hypothesized that NDMA precursors could be produced through metabolism of nitrogenous components and then gradually be biodegraded. To verify this hypothesis, six amino acids (AAs), peptone and ammonium were separately incubated with microorganism and NDMAFP was measured regularly. The average molar yield of the substrates to NDMAFP were 60–200 × 10⁻⁶ for the AAs, 350 × 10⁻⁶ for peptone under aerobic condition. The extracellular fraction with molecular weight (MW) less than 1 k Dalton contributed the majority to NDMAFP in the peptone experiment, followed by that with MW between 10 k and 0.22 μm and the intracellular materials. Dimethylamine and methylamine were detected during the experiments but their contribution to NDMAFP is quite limited. The results indicate that the nitrosamine precursors may not be the direct metabolite of AAs or peptones but the excretion of living bacteria or the components in dead bacteria body. Our results inferred that AA metabolism may give an NDMAFP of 0.12 nmol/L (maximum) or 0.09 nmol/L (average) in water under aerobic condition. This estimation of NDMAFP from AA metabolism can account for 38% (maximum) or 27% (average) of the median NDMAFP in waters of China (0.32 nmol/L) reported before.

Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location

Authors

Marika A. Schulhof Andrew E. Allen Eric E. Allen Natalie Mladenov John P. McCrow Natalie T. Jones Jessica Blanton Hamanda B. Cavalheri Drishti Kaul Celia C. Symons Jonathan B. Shurin

Warming, eutrophication (nutrient fertilization) and brownification (increased loading of allochthonous organic matter) are three global trends impacting lake ecosystems. However, the independent and synergistic effects of resource addition and warming on autotrophic and heterotrophic microorganisms are largely unknown. In this study, we investigate the independent and interactive effects of temperature, dissolved organic carbon (DOC, both allochthonous and autochthonous) and nitrogen (N) supply, in addition to the effect of spatial variables, on the composition, richness, and evenness of prokaryotic and eukaryotic microbial communities in lakes across elevation and N deposition gradients in the Sierra Nevada mountains of California, USA. We found that both prokaryotic and eukaryotic communities are structured by temperature, terrestrial (allochthonous) DOC and latitude. Prokaryotic communities are also influenced by total and aquatic (autochthonous) DOC, while eukaryotic communities are also structured by nitrate. Additionally, increasing N availability was associated with reduced richness of prokaryotic communities, and both lower richness and evenness of eukaryotes. We did not detect any synergistic or antagonistic effects as there were no interactions among temperature and resource variables. Together, our results suggest that (a) organic and inorganic resources, temperature, and geographic location (based on latitude and longitude) independently influence lake microbial communities; and (b) increasing N supply due to atmospheric N deposition may reduce richness of both prokaryotic and eukaryotic microbes, probably by reducing niche dimensionality. Our study provides insight into abiotic processes structuring microbial communities across environmental gradients and their potential roles in material and energy fluxes within and between ecosystems.

 

Measuring photosynthesis of both oxygenic and anoxygenic photosynthetic organisms using pulse amplitude modulation (PAM) fluorometry in wastewater ponds

Authors

P. Chandaravithoon, R. J. Ritchie & J. W. Runcie

Oxygenic photosynthesis can be measured easily using O₂ or CO₂ gas exchange, oxygen electrodes, Winkler titration, ¹⁴CO₂-fixation and by PAM (pulse amplitude modulation) fluorometry. PAM estimates the photosynthetic electron transport rate (ETR) by measuring the variable fluorescence of chlorophyll (Chl) a (> 695 nm) induced by absorption of blue or red light. Anoxygenic photosynthetic bacteria (APB) do not use water as an electron source and are typically photoheterotrophic rather than photoautotrophic and so ¹⁴CO₂ fixation is a misleading estimate of photosynthetic electron transport in APB photosynthesis. In vivo bacteriochlorophyll a (BChl a) absorbs blue light similar to Chl a but its characteristic longer-wavelength absorption is in the infrared and fluorescence is at > 800 nm. Blue light-induced PAM fluorescence can be used to measure the ETR in purple non-sulphur anoxygenic photobacteria and purple sulphur photobacteria because their RC-2 type BChl a complexes fluoresce similarly to PSII but at longer wavelengths than Chl a. Conventional PAM fluorometers using blue light cannot readily distinguish between oxygenic and RC-2 type anoxygenic photosynthesis because they use a simple > 700 nm highpass filter in front of the detector diode. We modified one fluorometer to use a 695–750-nm bandpass filter to measure Chl a fluorescence from PS-II, representing oxygenic photosynthesis. Similarly, we modified another fluorometer to use a highpass filter (> 830 nm) to measure BChl a fluorescence, representing anoxygenic photosynthesis. However, the fluorescence bands of Chl a and BChl a were found to be too wide to unambiguously distinguish between oxygenic and anoxygenic photosynthesis purely by fluorometry. Treatment with the specific PS-II inhibitor DCMU (Diuron) did enable discrimination of the two types of photosynthesis in a mixture of oxygenic and anoxygenic organisms. Ecological niches made up of both oxygenic and anoxygenic organisms such as microbial mats and hypereutrophic environments such as sewage ponds, wastewater ponds and prawn farm ponds are much more common than often realized. Anoxygenic photosynthesis in such systems is significant yet largely unquantified.

 

The Composition and Function of Microbiomes Within Microcystis Colonies Are Significantly Different Than Native Bacterial Assemblages in Two North American Lakes

Authors

Jennifer G. Jankowiak and Christopher J. Gobler

The toxic cyanobacterium Microcystis is one of the most pervasive harmful algal bloom (HAB) genera and naturally occurs in large colonies known to harbor diverse heterotrophic bacterial assemblages. While colony-associated microbiomes may influence Microcystis blooms, there remains a limited understanding of the structure and functional potential of these communities and how they may be shaped by changing environmental conditions. To address this gap, we compared the dynamics of Microcystis-attached (MCA), free-living (FL), and whole water microbiomes during Microcystis blooms using next-generation amplicon sequencing (16S rRNA), a predictive metagenome software, and other bioinformatic approaches. Microbiomes were monitored through high resolution spatial-temporal surveys across two North American lakes, Lake Erie (LE) and Lake Agawam (LA; Long Island, NY, United States) in 2017, providing the largest dataset of these fractions to date. Sequencing of 126 samples generated 7,922,628 sequences that clustered into 7,447 amplicon sequence variants (ASVs) with 100% sequence identity. Across lakes, the MCA microbiomes were significantly different than the FL and W fractions being significantly enriched in Gemmatimonadetes, Burkholderiaceae, Rhizobiales, and Cytophagales and depleted of Actinobacteria. Further, although MCA communities harbored > 900 unique ASVs, they were significantly less diverse than the other fractions with diversity inversely related to bloom intensity, suggesting increased selection pressure on microbial communities as blooms intensified. Despite taxonomic differences between lakes, predicted metagenomes revealed conserved functional potential among MCA microbiomes. MCA communities were significantly enriched in pathways involved in N and P cycling and microcystin-degradation. Taxa potentially capable of N₂-fixation were significantly enriched (p < 0.05) and up to four-fold more abundant within the MCA faction relative to other fractions, potentially aiding in the proliferation of Microcystis blooms during low N conditions. The MCA predicted metagenomes were conserved over 8 months of seasonal changes in temperature and N availability despite strong temporal succession in microbiome composition. Collectively, these findings indicate that Microcystis colonies harbor a statistically distinct microbiome with a conserved functional potential that may help facilitate bloom persistence under environmentally unfavorable conditions.

Interaction of bacterial communities and indicators of water quality in shoreline sand, sediment, and water of Lake Michigan

Authors

Meredith B. Nevers, Muruleedhara N. Byappanahalli, Cindy H. Nakatsu, Julie L. Kinzelman, Mantha S. Phanikumar, Dawn A. Shively, Ashley M. Spoljaric

Shoreline sand harbors high concentrations of fecal indicator bacteria (FIB) that may be resuspended into the water column through washing and resuspension. Studies have explored coastal processes that influence this sand-water flux for FIB, but little is known about how microbial markers of contamination or the bacterial community interact in the sand-water interface. In this study, we take a three-tiered approach to explore the relationship between bacteria in sand, sediment, and overlying water at three shoreline sites and two associated rivers along an extended freshwater shoreline. Samples were collected over two years and analyzed for FIB, two microbial source tracking (MST) markers (Catellicoccus marimammalium, Gull2; Bacteroides HF183), and targeted metagenomic 16S rRNA gene analysis. FIB was much higher in sand than in water at all three sites. Gull2 marker was abundant in shoreline sand and water while HF183 marker was mostly present in rivers. Overall bacterial communities were dissimilar between sand/sediment and water, indicating little interaction. Sediment composition was generally unfavorable to bacterial resuspension. Results show that FIB and MST markers were effective estimates of short-term conditions at these locations, and bacterial communities in sand and sediment reflected longer-term conditions. Findings are useful for locating contamination sources and targeting restoration by evaluating scope of shoreline degradation.

Different substrates within a lake harbour connected but specialised microbial communities

Authors

Ester M. Eckert, Stefano Amalfitano, Andrea Di Cesare, Caterina Manzari, Gianluca Corno & Diego Fontaneto

Natural water bodies contain physically interconnected habitats suitable for microbes, such as different water layers and substrates for biofilms. Yet, little is known on the extent to which microbial communities are shared between such habitats and whether differences and similarities are consistent between sites. Here we explicitly tested hypotheses on similarities between aquatic bacterial communities found floating in water, in association with daphnids and with copepods, within bottom sediments, and on littoral stones of a lake. Through high-throughput 16S rDNA amplicon sequencing, distinguishable patterns were retrieved between habitats. In particular, community composition was more similar between the two zooplankton taxa, between the two water depths, and was rather different in sediments, where a large fraction of the total diversity was present. Most bacterial taxa were restricted to one or few habitats, whereas only few were found as generalists on different habitats. Our results indicate a limited role of source–sink dynamics between habitats for aquatic bacteria. Similarly to patterns of diversity in larger organisms, community composition was different between habitats, potentially because of specific mechanisms creating and maintaining habitat filtering.