scholarly journals Microbial Community Dynamics and Assembly Follow Trajectories of an Early-Spring Diatom Bloom in a Semienclosed Bay

2018 ◽  
Vol 84 (18) ◽  
Author(s):  
Huajun Zhang ◽  
Kai Wang ◽  
Lixin Shen ◽  
Heping Chen ◽  
Fanrong Hou ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Nitrogen Metabolism ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Biogeochemical Cycles ◽  
Early Spring ◽  
Diatom Bloom ◽  
Ecological Processes ◽  
Content Type

ABSTRACTHarmful algal blooms (HABs) are serious ecological disasters in coastal areas, significantly influencing biogeochemical cycles driven by bacteria. The shifts in microbial communities during HABs have been widely investigated, but the assembly mechanisms of microbial communities during HABs are poorly understood. Here, using 16S rRNA gene amplicon sequencing, we analyzed the microbial communities during an early-spring diatom bloom, in order to investigate the dynamics of microbial assembly processes.Rhodobacteraceae,Flavobacteriaceae, andMicrobacteriaceaewere the main bacterial families during the bloom. The 30 most abundant operational taxonomic units (OTUs) segregated into 4 clusters according to specific bloom stages, exhibiting clear successional patterns during the bloom process. The succession of microbial communities correlated with changes in the dynamics of algal species. Based on the β-nearest taxon distance, we constructed a simulation model, which demonstrated that the assembly of microbial communities shifted from strong heterogenous selection in the early stage of the bloom to stochasticity in the middle stage and then to strong homogeneous selection in the late and after-bloom stages. These successions were driven mainly by chlorophyllacontents, which were affected mainly bySkeletonema costatum. Moreover, functional prediction of microbial communities showed that microbial metabolic functions were significantly related to nitrogen metabolism. In summary, our results clearly suggested a dominant role of determinacy in microbial community assembly in HABs and will facilitate deeper understanding of the ecological processes shaping microbial communities during the algal bloom process.IMPORTANCEHarmful algal blooms (HABs) significantly influence biogeochemical cycles driven by bacteria. The shifts in microbial communities during HABs have been studied intensively, but the assembly mechanisms of microbial communities during HABs are poorly understood, with limited investigation of the balance of deterministic and stochastic processes in shaping microbial communities in HABs. In this study, the dynamics and assembly of microbial communities in an early-spring diatom bloom process were investigated. Our data both confirm previously observed general microbial successional patterns and show new detailed mechanisms for microbial assembly in HABs. These results will facilitate deeper understanding of the ecological processes shaping microbial communities in HABs. In addition, predictions of metabolic potential in this study will facilitate understanding of the influence of HABs on nitrogen metabolism in marine environments.

scholarly journals Metatranscriptomic Evidence for Co-Occurring Top-Down and Bottom-Up Controls on Toxic Cyanobacterial Communities

2015 ◽  
Vol 81 (9) ◽  
pp. 3268-3276 ◽  
Author(s):  
Morgan M. Steffen ◽  
B. Shafer Belisle ◽  
Sue B. Watson ◽  
Gregory L. Boyer ◽  
Richard A. Bourbonniere ◽  
...  
Keyword(s):  
Microbial Community ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Lake Erie ◽  
Sequence Data ◽  
Top Down ◽  
Western Basin ◽  
Bottom Up ◽  
Content Type ◽  
Cyanobacterial Harmful Algal Blooms

ABSTRACTLittle is known about the molecular and physiological function of co-occurring microbes within freshwater cyanobacterial harmful algal blooms (cHABs). To address this, community metatranscriptomes collected from the western basin of Lake Erie during August 2012 were examined. Using sequence data, we tested the hypothesis that the activity of the microbial community members is independent of community structure. Predicted metabolic and physiological functional profiles from spatially distinct metatranscriptomes were determined to be ≥90% similar between sites. Targeted analysis ofMicrocystis aeruginosa, the historical causative agent of cyanobacterial harmful algal blooms over the past ∼20 years, as well as analysis ofPlanktothrix agardhiiandAnabaena cylindrica, revealed ongoing transcription of genes involved in microcystin toxin synthesis as well as the acquisition of both nitrogen and phosphorus, nutrients often implicated as independent bottom-up drivers of eutrophication in aquatic systems. Transcription of genes involved in carbon dioxide (CO2) concentration and metabolism also provided support for the alternate hypothesis that high-pH conditions and dense algal biomass result in CO2-limiting conditions that further favor cyanobacterial dominance. Additionally, the presence ofMicrocystis-specific cyanophage sequences provided preliminary evidence of possible top-down virus-mediated control of cHAB populations. Overall, these data provide insight into the complex series of constraints associated withMicrocystisblooms that dominate the western basin of Lake Erie during summer months, demonstrating that multiple environmental factors work to shape the microbial community.

scholarly journals Auxotrophic interactions: a stabilizing attribute of aquatic microbial communities?

2020 ◽  
Vol 96 (11) ◽  
Author(s):  
Winifred M Johnson ◽  
Harriet Alexander ◽  
Raven L Bier ◽  
Dan R Miller ◽  
Mario E Muscarella ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Theoretical Work ◽  
Microbial Interactions ◽  
Ecosystem Structure ◽  
Community Members ◽  
Aquatic Microorganisms ◽  
The Stability

ABSTRACT Auxotrophy, or an organism's requirement for an exogenous source of an organic molecule, is widespread throughout species and ecosystems. Auxotrophy can result in obligate interactions between organisms, influencing ecosystem structure and community composition. We explore how auxotrophy-induced interactions between aquatic microorganisms affect microbial community structure and stability. While some studies have documented auxotrophy in aquatic microorganisms, these studies are not widespread, and we therefore do not know the full extent of auxotrophic interactions in aquatic environments. Current theoretical and experimental work suggests that auxotrophy links microbial community members through a complex web of metabolic dependencies. We discuss the proposed ways in which auxotrophy may enhance or undermine the stability of aquatic microbial communities, highlighting areas where our limited understanding of these interactions prevents us from being able to predict the ecological implications of auxotrophy. Finally, we examine an example of auxotrophy in harmful algal blooms to place this often theoretical discussion in a field context where auxotrophy may have implications for the development and robustness of algal bloom communities. We seek to draw attention to the relationship between auxotrophy and community stability in an effort to encourage further field and theoretical work that explores the underlying principles of microbial interactions.

scholarly journals Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

scholarly journals Mapping the Distribution of Cysts from the Toxic Dinoflagellate Cochlodinium polykrikoides in Bloom-Prone Estuaries by a Novel FluorescenceIn SituHybridization Assay

2015 ◽  
Vol 82 (4) ◽  
pp. 1114-1125 ◽  
Author(s):  
Theresa K. Hattenrath-Lehmann ◽  
Yu Zhen ◽  
Ryan B. Wallace ◽  
Ying-Zhong Tang ◽  
Christopher J. Gobler
Keyword(s):  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Large Subunit ◽  
Cross Reactivity ◽  
Epifluorescence Microscopy ◽  
Lsu Rdna ◽  
Cochlodinium Polykrikoides ◽  
Content Type ◽  
Ecosystem Studies ◽  
Resting Cysts

ABSTRACTCochlodinium polykrikoidesis a cosmopolitan dinoflagellate that is notorious for causing fish-killing harmful algal blooms (HABs) across North America and Asia. While recent laboratory and ecosystem studies have definitively demonstrated thatCochlodiniumforms resting cysts that may play a key role in the dynamics of its HABs, uncertainties regarding cyst morphology and detection have prohibited even a rudimentary understanding of the distribution ofC. polykrikoidescysts in coastal ecosystems. Here, we report on the development of a fluorescencein situhybridization (FISH) assay using oligonucleotide probes specific for the large subunit (LSU) ribosomal DNA (rDNA) ofC. polykrikoides. The LSU rDNA-targeted FISH assay was used with epifluorescence microscopy and was iteratively refined to maximize the fluorescent reaction withC. polykrikoidesand minimize cross-reactivity. The final LSU rDNA-targeted FISH assay was found to quantitatively recover cysts made by North American isolates ofC. polykrikoidesbut not cysts formed by other common cyst-forming dinoflagellates. The method was then applied to identify and mapC. polykrikoidescysts across bloom-prone estuaries. Annual cyst and vegetative cell surveys revealed that elevated densities ofC. polykrikoidescysts (>100 cm−3) during the spring of a given year were spatially consistent with regions of dense blooms the prior summer. The identity of cysts in sediments was confirmed via independent amplification ofC. polykrikoidesrDNA. This study mappedC. polykrikoidescysts in a natural marine setting and indicates that the excystment of cysts formed by this harmful alga may play a key role in the development of HABs of this species.

scholarly journals Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities

2016 ◽  
Vol 83 (4) ◽  
Author(s):  
Nastassia V. Patin ◽  
Michelle Schorn ◽  
Kristen Aguinaldo ◽  
Tommie Lincecum ◽  
Bradley S. Moore ◽  
...  
Keyword(s):  
Microbial Community ◽  
Secondary Metabolites ◽  
Microbial Communities ◽  
Community Composition ◽  
Marine Sediments ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Next Generation ◽  
Content Type ◽  
Predatory Bacteria

ABSTRACT Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities. IMPORTANCE Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments.

scholarly journals Defining the Core Citrus Leaf- and Root-Associated Microbiota: Factors Associated with Community Structure and Implications for Managing Huanglongbing (Citrus Greening) Disease

2017 ◽  
Vol 83 (11) ◽  
Author(s):  
Ryan A. Blaustein ◽  
Graciela L. Lorca ◽  
Julie L. Meyer ◽  
Claudio F. Gonzalez ◽  
Max Teplitski
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Illumina Sequencing ◽  
Symptom Severity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
The Core ◽  
Symptom Progression

ABSTRACTStable associations between plants and microbes are critical to promoting host health and productivity. The objective of this work was to test the hypothesis that restructuring of the core microbiota may be associated with the progression of huanglongbing (HLB), the devastating citrus disease caused byLiberibacter asiaticus,Liberibacter americanus, andLiberibacter africanus. The microbial communities of leaves (n= 94) and roots (n= 79) from citrus trees that varied by HLB symptom severity, cultivar, location, and season/time were characterized with Illumina sequencing of 16S rRNA genes. The taxonomically rich communities contained abundant core members (i.e., detected in at least 95% of the respective leaf or root samples), some overrepresented site-specific members, and a diverse community of low-abundance variable taxa. The composition and diversity of the leaf and root microbiota were strongly associated with HLB symptom severity and location; there was also an association with host cultivar. The relative abundance ofLiberibacterspp. among leaf microbiota positively correlated with HLB symptom severity and negatively correlated with alpha diversity, suggesting that community diversity decreases as symptoms progress. Network analysis of the microbial community time series identified a mutually exclusive relationship betweenLiberibacterspp. and members of theBurkholderiaceae,Micromonosporaceae, andXanthomonadaceae. This work confirmed several previously described plant disease-associated bacteria, as well as identified new potential implications for biological control. Our findings advance the understanding of (i) plant microbiota selection across multiple variables and (ii) changes in (core) community structure that may be a precondition to disease establishment and/or may be associated with symptom progression.IMPORTANCEThis study provides a comprehensive overview of the core microbial community within the microbiomes of plant hosts that vary in extent of disease symptom progression. With 16S Illumina sequencing analyses, we not only confirmed previously described bacterial associations with plant health (e.g., potentially beneficial bacteria) but also identified new associations and potential interactions between certain bacteria and an economically important phytopathogen. The importance of core taxa within broader plant-associated microbial communities is discussed.

scholarly journals Microbial and chemical dynamics of a toxic dinoflagellate bloom

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9493
Author(s):  
Nastassia V. Patin ◽  
Emily Brown ◽  
Gabriella Chebli ◽  
Claire Garfield ◽  
Julia Kubanek ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Economic Damage ◽  
Sequence Variant ◽  
Toxic Dinoflagellate ◽  
Bloom Formation ◽  
Intracellular Metabolite Pools ◽  
Domain Level ◽  
Dinoflagellate Bloom

Harmful Algal Blooms (HABs) exert considerable ecological and economic damage and are becoming increasingly frequent worldwide. However, the biological factors underlying HABs remain uncertain. Relationships between algae and bacteria may contribute to bloom formation, strength, and duration. We investigated the microbial communities and metabolomes associated with a HAB of the toxic dinoflagellate Karenia brevis off the west coast of Florida in June 2018. Microbial communities and intracellular metabolite pools differed based on both bacterial lifestyle and bloom level, suggesting a complex role for blooms in reshaping microbial processes. Network analysis identified K. brevis as an ecological hub in the planktonic ecosystem, with significant connections to diverse microbial taxa. These included four flavobacteria and one sequence variant unidentified past the domain level, suggesting uncharacterized diversity in phytoplankton-associated microbial communities. Additionally, intracellular metabolomic analyses associated high K. brevis levels with higher levels of aromatic compounds and lipids. These findings reveal water column microbial and chemical characteristics with potentially important implications for understanding HAB onset and duration.

scholarly journals Regular Biochar and Bacteria-Inoculated Biochar Alter the Composition of the Microbial Community in the Soil of a Chinese Fir Plantation

Forests ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 951
Author(s):  
Liguo Song ◽  
Lingyu Hou ◽  
Yongqiang Zhang ◽  
Zhichao Li ◽  
Wenzheng Wang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Rhizosphere Soil ◽  
Soil Microbial Communities ◽  
Principal Component ◽  
Nutrient Content ◽  
Chinese Fir ◽  
Bulk Soil ◽  
Ecological Processes ◽  
Chinese Fir Plantation

Biochar is a promising material for the improvement of soil quality. However, studies on biochar have mostly been carried out in laboratory conditions or have focused on agricultural aspects. The impacts of the application of biochar on soil characteristics and related ecological processes of the forest ecosystem have not been fully resolved. In this study, we investigated the effects of regular biochar and bacteria-loaded biochar on the microbial communities in the bulk soil and the rhizosphere soil of an annual Chinese fir plantation. In early spring (April), the two types of biochar were added to the soil at the rates of 2.22 t·ha−1, 4.44 t·ha−1, 6.67 t·ha−1, 8.89 t·ha−1, and 11.11 t·ha−1 by ring furrow application around the seedlings, and soil samples were collected at the end of autumn (November). The results showed that biochar addition increased the soil nutrient content and promoted the growth and diversity of soil microbial communities. The diversity of soil fungi was significantly increased, and the diversity of soil bacteria was significantly decreased. Principal component analysis under the different biochar types and application rates demonstrated that microbial communities differed significantly between the treatments and controls and that the effect of biochar on the microbial community of the bulk soil was more significant than that of the rhizosphere soil. Under the same dosage, the effect of bacteria-loaded biochar on soil was more significant than that of regular biochar.

scholarly journals Microbial Community Dynamics of an Urban Drinking Water Distribution System Subjected to Phases of Chloramination and Chlorination Treatments

2012 ◽  
Vol 78 (22) ◽  
pp. 7856-7865 ◽  
Author(s):  
Chiachi Hwang ◽  
Fangqiong Ling ◽  
Gary L. Andersen ◽  
Mark W. LeChevallier ◽  
Wen-Tso Liu
Keyword(s):  
Drinking Water ◽  
Microbial Community ◽  
Microbial Communities ◽  
Distribution Systems ◽  
Water Distribution ◽  
Microbial Populations ◽  
Rrna Gene ◽  
Source Water ◽  
Content Type ◽  
Drinking Water Distribution

ABSTRACTWater utilities in parts of the U.S. control microbial regrowth in drinking water distribution systems (DWDS) by alternating postdisinfection methods between chlorination and chloramination. To examine how this strategy influences drinking water microbial communities, an urban DWDS (population ≅ 40,000) with groundwater as the source water was studied for approximately 2 years. Water samples were collected at five locations in the network at different seasons and analyzed for their chemical and physical characteristics and for their microbial community composition and structure by examining the 16S rRNA gene via terminal restriction fragment length polymorphism and DNA pyrosequencing technology. Nonmetric multidimension scaling and canonical correspondence analysis of microbial community profiles could explain >57% of the variation. Clustering of samples based on disinfection types (free chlorine versus combined chlorine) and sampling time was observed to correlate to the shifts in microbial communities. Sampling location and water age (<21.2 h) had no apparent effects on the microbial compositions of samples from most time points. Microbial community analysis revealed that among major core populations,Cyanobacteria,Methylobacteriaceae,Sphingomonadaceae, andXanthomonadaceaewere more abundant in chlorinated water, andMethylophilaceae,Methylococcaceae, andPseudomonadaceaewere more abundant in chloraminated water. No correlation was observed with minor populations that were detected frequently (<0.1% of total pyrosequences), which were likely present in source water and survived through the treatment process. Transient microbial populations includingFlavobacteriaceaeandClostridiaceaewere also observed. Overall, reversible shifts in microbial communities were especially pronounced with chloramination, suggesting stronger selection of microbial populations from chloramines than chlorine.

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