Species sorting along a subsidy gradient alters community stability

The movement of resources between terrestrial and aquatic habitats has strong effects on ecological processes in recipient ecosystems. Allochthonous inputs modify the quality and quantity of the available resource pool in ways that may alter the composition and stability of recipient communities. Inputs of terrestrial dissolved organic carbon (tDOC) into aquatic ecosystems represent a large influx of resources that has the potential to affect local communities, especially microorganisms. To evaluate the effects terrestrial inputs on aquatic microbial community composition and stability, we manipulated the supply rate of tDOC to a set of experimental ponds. Along the tDOC supply gradient, we measured changes in diversity and taxon-specific changes in abundance and activity. We then determined community stability by perturbing each pond using a pulse of inorganic nutrients and measuring changes in composition and activity (i.e., responsiveness) along the gradient. Terrestrial DOC supply significantly altered the composition of the active microbial community. The composition of the active bacterial community changed via decreases in richness and evenness as well as taxon-specific changes in abundance and activity indicating species sorting along the gradient. Likewise, the responsiveness of the active bacterial community decreased along the gradient, which led to a more stable active community. We did not, however, observe these changes in diversity and stability in the total community (i.e., active and inactive organisms), which suggests that tDOC supply modifies microbial community stability through functional not structural changes. Together, these results show that altered aquatic terrestrial linkages can have profound effects on the activity and stability of the base of the food web and thus can alter ecosystem functioning.

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Selective Bacterial Community Enrichment Between the Pitcher Plants Sarracenia Minor and Sarracenia Flava

10.21203/rs.3.rs-55560/v1 ◽

2020 ◽

Author(s):

Nikolas M. Stasulli ◽

Scott M. Yourstone ◽

Ilon Weinstein ◽

Elizabeth Ademski ◽

Elizabeth A. Shank

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Prey Availability ◽

Microbial Community Composition ◽

Geographic Location ◽

Rrna Gene ◽

Natural Ecosystems ◽

Community Members ◽

Pitcher Plants ◽

Naturally Occurring

Abstract BackgroundThe interconnected and overlapping habitats present in natural ecosystems remain a challenge in determining the forces driving microbial community composition. The cup-like leaf structures of some carnivorous plants, including the family Sarraceniaceae, are self-contained ecological habitats that represent systems for exploring such microbial ecology questions. We investigated whether Sarracenia minor and Sarracenia flava, when sampled at the same geographic location and time, cultivate unique microbiota; an indication of biotic selection of microbes due to eliminating many of the environmental variable present in other studies comparing samples harvested over several time points. ResultsDNA was extracted from the decomposing detritus trapped in the base of each Sarracenia leaf pitcher. We profiled a portion of the 16S rRNA gene across the bacterial community members present in this detritus using Illumina MiSeq technology. We identified a surprising amount of diversity within each pitcher, but also discovered that the two Sarracenia species each contained distinct, enriched microbial community members. This suggests a non-random establishment of microbial communities within these two Sarracenia species.ConclusionsOverall, our results indicate that microbial selection is occurring within the pitchers of these two closely related plant species, which is not due to factors such as geographic location, weather, or prey availability. This suggests that specific features of S. minor and S. flava may play a role in fostering specific insect-decomposing microbiomes. These naturally occurring microbial ecosystems can be developed to answer important questions about microbial community succession, disruption, and member contributions to the community. This study will help further establish carnivorous pitcher plants as a model system for studying confined, naturally occurring bacterial communities.

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Ecology and Host Identity Outweigh Evolutionary History in Shaping the Bat Microbiome

mSystems ◽

10.1128/msystems.00511-19 ◽

2019 ◽

Vol 4 (6) ◽

Cited By ~ 5

Author(s):

Holly L. Lutz ◽

Elliot W. Jackson ◽

Paul W. Webala ◽

Waswa S. Babyesiza ◽

Julian C. Kerbis Peterhans ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Community Composition ◽

Evolutionary History ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Anatomical Site ◽

Skin Microbiota ◽

Host Identity ◽

Host Ecology

ABSTRACT Recent studies of mammalian microbiomes have identified strong phylogenetic effects on bacterial community composition. Bats (Mammalia: Chiroptera) are among the most speciose mammals on the planet and the only mammal capable of true flight. We examined 1,236 16S rRNA amplicon libraries of the gut, oral, and skin microbiota from 497 Afrotropical bats (representing 9 families, 20 genera, and 31 species) to assess the extent to which host ecology and phylogeny predict microbial community similarity in bats. In contrast to recent studies of host-microbe associations in other mammals, we found no correlation between chiropteran phylogeny and bacterial community dissimilarity across the three anatomical sites sampled. For all anatomical sites, we found host species identity and geographic locality to be strong predictors of microbial community composition and observed a positive correlation between elevation and bacterial richness. Last, we identified significantly different bacterial associations within the gut microbiota of insectivorous and frugivorous bats. We conclude that the gut, oral, and skin microbiota of bats are shaped predominantly by ecological factors and do not exhibit the same degree of phylosymbiosis observed in other mammals. IMPORTANCE This study is the first to provide a comprehensive survey of bacterial symbionts from multiple anatomical sites across a broad taxonomic range of Afrotropical bats, demonstrating significant associations between the bat microbiome and anatomical site, geographic locality, and host identity—but not evolutionary history. This study provides a framework for future systems biology approaches to examine host-symbiont relationships across broad taxonomic scales, emphasizing the need to elucidate the interplay between host ecology and evolutionary history in shaping the microbiome of different anatomical sites.

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Colonization in the Photic Zone and Subsequent Changes during Sinking Determine Bacterial Community Composition in Marine Snow

Applied and Environmental Microbiology ◽

10.1128/aem.02570-14 ◽

2014 ◽

Vol 81 (4) ◽

pp. 1463-1471 ◽

Cited By ~ 45

Author(s):

Stefan Thiele ◽

Bernhard M. Fuchs ◽

Rudolf Amann ◽

Morten H. Iversen

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Microbial Communities ◽

Community Composition ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Marine Snow ◽

Free Living ◽

Fluorescence Maximum

ABSTRACTDue to sampling difficulties, little is known about microbial communities associated with sinking marine snow in the twilight zone. A drifting sediment trap was equipped with a viscous cryogel and deployed to collect intact marine snow from depths of 100 and 400 m off Cape Blanc (Mauritania). Marine snow aggregates were fixed and washedin situto prevent changes in microbial community composition and to enable subsequent analysis using catalyzed reporter deposition fluorescencein situhybridization (CARD-FISH). The attached microbial communities collected at 100 m were similar to the free-living community at the depth of the fluorescence maximum (20 m) but different from those at other depths (150, 400, 550, and 700 m). Therefore, the attached microbial community seemed to be “inherited” from that at the fluorescence maximum. The attached microbial community structure at 400 m differed from that of the attached community at 100 m and from that of any free-living community at the tested depths, except that collected near the sediment at 700 m. The differences between the particle-associated communities at 400 m and 100 m appeared to be due to internal changes in the attached microbial community rather thande novocolonization, detachment, or grazing during the sinking of marine snow. The new sampling method presented here will facilitate future investigations into the mechanisms that shape the bacterial community within sinking marine snow, leading to better understanding of the mechanisms which regulate biogeochemical cycling of settling organic matter.

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Effect of Methane Inhibitors on Ruminal Microbiota During Early Life and Its Relationship With Ruminal Metabolism and Growth in Calves

Frontiers in Microbiology ◽

10.3389/fmicb.2021.710914 ◽

2021 ◽

Vol 12 ◽

Author(s):

Omar Cristobal-Carballo ◽

Susan A. McCoard ◽

Adrian L. Cookson ◽

Siva Ganesh ◽

Katherine Lowe ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Community Composition ◽

Early Life ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Metabolite Profile ◽

Treatment Groups ◽

Methanogen Community ◽

And Performance

The present study aimed to determine whether dietary supplementation with methanogen inhibitors during early life may lead to an imprint on the rumen microbial community and change the rumen function and performance of calves to 49-weeks of rearing. Twenty-four 4-day-old Friesian x Jersey cross calves were randomly assigned into a control and a treatment group. Treated calves were fed a combination of chloroform (CF) and 9,10-anthraquinone (AQ) in the solid diets during the first 12 weeks of rearing. Afterward, calves were grouped by treatments until week 14, and then managed as a single group on pasture. Solid diets and water were offered ad libitum. Methane measurements, and sample collections for rumen metabolite and microbial community composition were carried out at the end of weeks 2, 4, 6, 8, 10, 14, 24 and 49. Animal growth and dry matter intake (DMI) were regularly monitored over the duration of the experiment. Methane emissions decreased up to 90% whilst hydrogen emissions increased in treated compared to control calves, but only for up to 2 weeks after treatment cessation. The near complete methane inhibition did not affect calves’ DMI and growth. The acetate:propionate ratio decreased in treated compared to control calves during the first 14 weeks but was similar at weeks 24 and 49. The proportions of Methanobrevibacter and Methanosphaera decreased in treated compared to control calves during the first 14 weeks; however, at week 24 and 49 the archaea community was similar between groups. Bacterial proportions at the phylum level and the abundant bacterial genera were similar between treatment groups. In summary, methane inhibition increased hydrogen emissions, altered the methanogen community and changed the rumen metabolite profile without major effects on the bacterial community composition. This indicated that the main response of the bacterial community was not a change in composition but rather a change in metabolic pathways. Furthermore, once methane inhibition ceased the methanogen community, rumen metabolites and hydrogen emissions became similar between treatment groups, indicating that perhaps using the treatments tested in this study, it is not possible to imprint a low methane microbiota into the rumen in the solid feed of pre-weaned calves.

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Bacterial and Fungal Endophytic Microbiomes of Salicornia europaea

Applied and Environmental Microbiology ◽

10.1128/aem.00305-19 ◽

2019 ◽

Vol 85 (13) ◽

Cited By ~ 13

Author(s):

Bliss Ursula Furtado ◽

Marcin Gołębiewski ◽

Monika Skorupa ◽

Piotr Hulisz ◽

Katarzyna Hrynkiewicz

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Microbial Community Composition ◽

Operational Taxonomic Unit ◽

Amplicon Sequencing ◽

Salicornia Europaea ◽

Core Microbiome ◽

Plant Organs ◽

Content Type ◽

Microbial Groups

ABSTRACT We examined Salicornia europaea, a nonmycorrhizal halophyte associated with specific and unique endophytic bacteria and fungi. The microbial community structure was analyzed at two sites differing in salinization history (anthropogenic and naturally saline site), in contrasting seasons (spring and fall) and in two plant organs (shoots and roots) via 16S rRNA and internal transcribed spacer amplicon sequencing. We observed distinct communities at the two sites, and in shoots and roots, while the season was of no importance. The bacterial community was less diverse in shoot libraries than in roots, regardless of the site and season, whereas no significant differences were observed for the fungal community. Proteobacteria and Bacteroidetes dominated bacterial assemblages, and Ascomycetes were the most frequent fungi. A root core microbiome operational taxonomic unit belonging to the genus Marinimicrobium was identified. We detected a significant influence of the Salicornia bacterial community on the fungal one by means of cocorrespondence analysis. In addition, pathways and potential functions of the bacterial community in Salicornia europaea were inferred and discussed. We can conclude that bacterial and fungal microbiomes of S. europaea are determined by the origin of salinity at the sites. Bacterial communities seemed to influence fungal ones, but not the other way around, which takes us closer to understanding of interactions between the two microbial groups. In addition, the plant organs of the halophyte filter the microbial community composition. IMPORTANCE Endophytes are particularly fascinating because of their multifaceted lifestyle, i.e., they may exist as either free-living soil microbes or saprobic ones or pathogens. Endophytic communities of halophytes may be different than those in other plants because salinity acts as an environmental filter. At the same time, they may contribute to the host’s adaptation to adverse environmental conditions, which may be of importance in agriculture.

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High Carbon Load in Food Processing Industrial Wastewater is a Driver for Metabolic Competition in Aerobic Granular Sludge

Frontiers in Environmental Science ◽

10.3389/fenvs.2021.735607 ◽

2021 ◽

Vol 9 ◽

Author(s):

Ana M. S. Paulo ◽

Catarina L. Amorim ◽

Joana Costa ◽

Daniela P. Mesquita ◽

Eugénio C. Ferreira ◽

...

Keyword(s):

Microbial Community ◽

Industrial Wastewater ◽

Structural Changes ◽

Microbial Community Composition ◽

Granular Sludge ◽

Aerobic Granular Sludge ◽

Organic Loading Rate ◽

Second Phase ◽

Metabolic Versatility ◽

Two Phases

Aerobic granular sludge (AGS) processes are among the most robust wastewater treatments. One of their greatest advantages is related to the granules multi-layered structure, which creates a protective barrier against organic shock loads and variable wastewater composition, particularly attractive for the treatment of industrial wastewater. However, when treating a wastewater with variable and complex composition, the difficulty in identifying factors that most affect a specific biological process increases. In this study, the effect of organic loading rate (OLR), namely carbon content, on nitrification in an AGS process treating fish canning wastewater was investigated. Besides process performance, also biomass structural changes, and microbial community composition were analysed. Reactor operation lasted for 107 days and was divided in three phases during which different OLR and C/N ratios were applied. A higher OLR was applied during the first two phases (ca. 1.1 and 1.5 kg COD m−3 day−1, respectively) compared to the third phase (between 0.12 and 0.78 kg COD m−3 day−1) and the C/N ratios also varied (ca. 4.4, 7.8, and 2.9, respectively). Throughout the operation, COD concentration in the outlet was lower than 100 mg O2 L−1. Nitrification was inhibited during the second phase and recovered afterwards. Principal component analysis (PCA) of quantitative image analysis (QIA) and performance data allowed to distinguish process changes over the three operational phases. During the first two phases, the decrease in the biomass robustness occurred, but recovered during the last phase, indicating that the high content of organic matter had possibly an effect on the aerobic granules structural characteristics. The composition of the AGS microbiome did not change substantially after the end of the higher OLR periods. The main microbial diversity shifts were mostly associated to adaptation to higher or lower carbon availability. Bacteria and inferred enzymes associated to nitrogen and phosphorous removal were identified. Chryseobacterium, a bacterium with high metabolic versatility, was able to adapt to the organic shock load, becoming dominant over operation. Despite the variable composition of the fish canning wastewater, carbon was identified as the main driver for nitrification inhibition, while promoting changes in the physical characteristics and on the microbial community of granules.

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Bacterial community composition and diversity of two different forms of an organic residue of bioenergy crop

PeerJ ◽

10.7717/peerj.6768 ◽

2019 ◽

Vol 7 ◽

pp. e6768

Author(s):

Matheus A.P. Cipriano ◽

Afnan K.A. Suleiman ◽

Adriana P.D. da Silveira ◽

Janaína B. do Carmo ◽

Eiko E. Kuramae

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

16S Rrna ◽

Community Composition ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Nitrous Oxide Emissions ◽

Rrna Gene ◽

Bacterial Strains ◽

Microbial Composition

The use of residue of sugarcane ethanol industry named vinasse in fertirrigation is an established and widespread practice in Brazil. Both non-concentrated vinasse (NCV) and concentrated vinasse (CV) are used in fertirrigation, particularly to replace the potassium fertilizer. Although studies on the chemical and organic composition of vinasse and their impact on nitrous oxide emissions when applied in soil have been carried out, no studies have evaluated the microbial community composition and diversity in different forms of vinasse. We assessed the bacterial community composition of NCV and CV by non-culturable and culturable approaches. The non-culturable bacterial community was assessed by next generation sequencing of the 16S rRNA gene and culturable community by isolation of bacterial strains and molecular and biochemical characterization. Additionally, we assessed in the bacterial strains the presence of genes of nitrogen cycle nitrification and denitrification pathways. The microbial community based on16S rRNAsequences of NCV was overrepresented by Bacilli and Negativicutes while CV was mainly represented by Bacilli class. The isolated strains from the two types of vinasse belong to class Bacilli, similar toLysinibacillus, encode fornirKgene related to denitrification pathway. This study highlights the bacterial microbial composition particularly in CV what residue is currently recycled and recommended as a sustainable practice in sugarcane cultivation in the tropics.

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Microbial community composition and abundance after millennia of submarine permafrost warming

Biogeosciences ◽

10.5194/bg-16-3941-2019 ◽

2019 ◽

Vol 16 (19) ◽

pp. 3941-3958 ◽

Cited By ~ 1

Author(s):

Julia Mitzscherling ◽

Fabian Horn ◽

Maria Winterfeld ◽

Linda Mahler ◽

Jens Kallmeyer ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Community Composition ◽

Pore Water ◽

Negative Correlation ◽

Microbial Community Composition ◽

Microbial Abundance ◽

Bacterial Gene ◽

Permafrost Warming

Abstract. Warming of the Arctic led to an increase in permafrost temperatures by about 0.3 ∘C during the last decade. Permafrost warming is associated with increasing sediment water content, permeability, and diffusivity and could in the long term alter microbial community composition and abundance even before permafrost thaws. We studied the long-term effect (up to 2500 years) of submarine permafrost warming on microbial communities along an onshore–offshore transect on the Siberian Arctic Shelf displaying a natural temperature gradient of more than 10 ∘C. We analysed the in situ development of bacterial abundance and community composition through total cell counts (TCCs), quantitative PCR of bacterial gene abundance, and amplicon sequencing and correlated the microbial community data with temperature, pore water chemistry, and sediment physicochemical parameters. On timescales of centuries, permafrost warming coincided with an overall decreasing microbial abundance, whereas millennia after warming microbial abundance was similar to cold onshore permafrost. In addition, the dissolved organic carbon content of all cores was lowest in submarine permafrost after millennial-scale warming. Based on correlation analysis, TCC, unlike bacterial gene abundance, showed a significant rank-based negative correlation with increasing temperature, while bacterial gene copy numbers showed a strong negative correlation with salinity. Bacterial community composition correlated only weakly with temperature but strongly with the pore water stable isotopes δ18O and δD, as well as with depth. The bacterial community showed substantial spatial variation and an overall dominance of Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadetes, and Proteobacteria, which are amongst the microbial taxa that were also found to be active in other frozen permafrost environments. We suggest that, millennia after permafrost warming by over 10 ∘C, microbial community composition and abundance show some indications for proliferation but mainly reflect the sedimentation history and paleoenvironment and not a direct effect through warming.

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Effect of River Ecological Restoration on Biofilm Microbial Community Composition

Water ◽

10.3390/w11061244 ◽

2019 ◽

Vol 11 (6) ◽

pp. 1244 ◽

Cited By ~ 4

Author(s):

Qiaoyan Lin ◽

Raju Sekar ◽

Rob Marrs ◽

Yixin Zhang

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Microbial Communities ◽

Community Composition ◽

Organic Pollutants ◽

Habitat Restoration ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Reference Conditions ◽

Urban Rivers

Across the world, there have been increasing attempts to restore good ecological condition to degraded rivers through habitat restoration. Microbial communities developing as biofilms play an important role in river ecosystem functioning by driving organic matter decomposition and ecosystem respiration. However, little is known about the structure and function of microbial communities in riverine systems and how these change when habitat restoration is implemented. Here, we compared the biofilm bacterial community composition using 16S rRNA genes targeted high-throughput Illumina Miseq sequencing in three river types, degraded urban rivers, urban rivers undergoing habitat restoration and forested rivers (our reference conditions). We aimed to determine: (i) the biofilm bacterial community composition affected by habitat restoration (ii) the difference in bacterial diversity in restored rivers, and (iii) correlations between environmental variables and bacterial community composition. The results showed that both water quality and biofilm bacterial community structure were changed by habitat restoration. In rivers where habitat had been restored, there was an increase in dissolved oxygen, a reduction in organic pollutants, a reduction in bacterial diversity and a related developing pattern of microbial communities, which is moving towards that of the reference conditions (forested rivers). River habitat management stimulated the processing of organic pollutants through the variation in microbial community composition, however, a big difference in bacterial structure still existed between the restored rivers and the reference forest rivers. Thus, habitat restoration is an efficient way of modifying the biofilm microbial community composition for sustainable freshwater management. It will, however, take a much longer time for degraded rivers to attain a similar ecosystem quality as the “pristine” forest sites than the seven years of restoration studied here.

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Microbial communities in soil macro-aggregates respire less, are more diverse and stable across successional and geographical gradients

10.5194/egusphere-egu21-16011 ◽

2021 ◽

Author(s):

Daquan Sun ◽

Gerrit Angst ◽

Jan Frouz

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Microbial Respiration ◽

Soil Aggregates ◽

Sampling Site ◽

Microbial Community Composition ◽

Dominant Factor ◽

Community Stability ◽

Community Structures ◽

Soil Fractions

<p>The stability of soil organic carbon is empirically believed to relate to the location of soil microorganisms inside or between aggregates. However, there are knowledge gaps about how micro-niches shape the microbial community composition and activity and how these effects vary between various soils. Here, we investigate fungal and bacterial community structures (composition and biomass), networks, and respiration in individual micro-niches between and inside soil aggregates using seven different chronosequences (both primary and secondary successions covering sites from pioneer stages to well-developed ecosystems) from a maritime climate in Belgium to a more continental climate in Hungary. We show that while the sampling site is the most crucial factor in shaping microbial community structures, soil aggregates are often more important than succession age and vegetation in differentiating major microbial taxa. Soil fractions are also the dominant factor affecting microbial biomass along the individual chronosequences. Specifically, macro-aggregates often have more variable &#945;-diversities and high microbial community stability, accompanied by low microbial respiration rates. Although the other isolated soil fractions have similar microbial diversities as macro-aggregates, they feature unstable microbial communities with a higher respiration rate. The isolated primary particles have more stable bacterial communities in secondary than primary successions. We, thus, provide a mechanism for interpreting the links between soil microsite heterogeneity, microbial community stability, and microbial respiration.&#160;</p>

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