All-In-One: Microbial Response to Natural and Anthropogenic Forcings in a Coastal Mediterranean Ecosystem, the Syracuse Bay (Ionian Sea, Italy)

Bacterial and phytoplankton communities are known to be in close relationships, but how natural and anthropogenic stressors can affect their dynamics is not fully understood. To study the response of microbial communities to environmental and human-induced perturbations, phytoplankton and bacterial communities were seasonally monitored in a Mediterranean coastal ecosystem, Syracuse Bay, where multiple conflicts co-exist. Quali-quantitative, seasonal surveys of the phytoplankton communities (diatoms, dinoflagellates and other taxa), the potential microbial enzymatic activity rates (leucine aminopeptidase, beta-glucosidase and alkaline phosphatase) and heterotrophic culturable bacterial abundance, together with the thermohaline structure and trophic status in terms of nutrient concentrations, phytoplankton biomass (as Chlorophyll-a), and total suspended and particulate organic matter, were carried out. The aim was to integrate microbial community dynamics in the context of the environmental characterization and disentangle microbial patterns related to natural changes from those driven by the anthropic impact on this ecosystem. In spite of the complex relationships between the habitat characteristics, microbial community abundance and metabolic potential, in Syracuse Bay, the availability of organic substrates differently originated by the local conditions appeared to drive the distribution and activity of microbial assemblage. A seasonal pattern of microbial abundances was observed, with the highest concentrations of phytoplankton in spring and low values in winter, whereas heterotrophic bacteria were more abundant during the autumn period. The autumn peaks of the rates of enzymatic activities suggested that not only phytoplankton-derived but also allochthonous organic polymers strongly stimulated microbial metabolism. Increased microbial response in terms of abundance and metabolic activities was detected especially at the sites directly affected by organic matter inputs related to agriculture or aquaculture activities. Nitrogen salts such as nitrate, rather than orthophosphate, were primary drivers of phytoplankton growth. This study also provides insights on the different seasonal scenarios of water quality in Syracuse Bay, which could be helpful for management plans of this Mediterranean coastal environment.

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Dissolved organic matter as P source for biofilms in two contrasting low-order streams

Fundamental and Applied Limnology / Archiv für Hydrobiologie ◽

10.1127/fal/2019/1234 ◽

2019 ◽

Vol 193 (2) ◽

pp. 131-142

Author(s):

Verónica Díaz-Villanueva

Keyword(s):

Organic Matter ◽

Dissolved Organic Matter ◽

Deciduous Forest ◽

Spatial Scales ◽

Algal Species ◽

Community Level ◽

Nutrient Concentrations ◽

Organic Substrates ◽

One Year ◽

Forest Streams

Forest streams receive large amounts of leaves whose leachates are an important source of dissolved organic matter (DOM), providing not only carbon but also organic nutrients to the microbial communities in streams. I carried out a field study to evaluate the effect of different DOM concentrations on the biofilm structure and functional traits in two similar forest streams belonging to the same catchment. I compared biofilm biomass and nutri- ent content throughout one year, algal species composition, and biofilm community-level physiological profiles in two streams with different DOM concentration and aromaticity. Dissolved nutrient concentrations were higher in the stream with higher DOM concentration, with a concomitant higher biofilm biomass, and there was also a temporal pattern, with higher values during the autumn. Phosphorus content in biofilms was also higher in the high DOM stream, coincidently with a higher capacity of the community to utilize organic P source (glucose-1-P) as a substrate. In contrast, the biofilms from the stream with lower DOM concentrations preferentially used N-organic substrates (amino acids and amines). These results reveal that the biofilms of forest streams make use of organic matter nutrients, so that streams with different DOM loads may differ in biofilm biomass due to changes in both bacterial and autotrophic biomass. In addition, biofilm dynamics may be related to forest phenology, as the highest OM input in this deciduous forest is represented by tree leaves, which supply DOM through leachates, and in particular, with P-rich leachates. In conclusion, different DOM concentrations in two nearby streams led to differences in the community-level physiological profile, as has been previously demonstrated at larger spatial scales in oceans, lakes and along larger rivers.

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Dissimilar bacterial and fungal decomposer communities across rich to poor fen peatlands exhibit functional redundancy

Canadian Journal of Soil Science ◽

10.4141/cjss-2014-062 ◽

2015 ◽

Vol 95 (3) ◽

pp. 219-230 ◽

Cited By ~ 4

Author(s):

Kristine M. Haynes ◽

Michael D. Preston ◽

James W. McLaughlin ◽

Kara Webster ◽

Nathan Basiliko

Keyword(s):

Organic Matter ◽

Microbial Communities ◽

Environmental Changes ◽

Functional Redundancy ◽

Organic Substrates ◽

Metabolic Potential ◽

Vegetation Communities ◽

Chemical Complexity ◽

Poor Fen

Haynes, K. M., Preston, M. D., McLaughlin, J. W., Webster, K. and Basiliko, N. 2015. Dissimilar bacterial and fungal decomposer communities across rich to poor fen peatlands exhibit functional redundancy. Can. J. Soil Sci. 95: 219–230. Climatic and environmental changes can lead to shifts in the dominant vegetation communities present in northern peatland ecosystems, including from Sphagnum- to vascular-dominated systems. Such shifts in vegetation result in changes to the chemical quality of carbon substrates for soil microbial decomposers, with leaves and roots deposited in the peat surface and subsurface that potentially decompose faster. This study characterized the bacterial and fungal communities present along a nutrient gradient ranging from rich to poor fen peatlands and assessed the metabolic potential of these communities to mineralize a variety of organic matter substrates of varying chemical complexity using substrate-induced respiration (SIR) assays. Distinct microbial communities existed between rich, intermediate and poor fens, but SIR in each of the three sites exhibited the same pattern of carbon mineralization, providing support for the concept of functional redundancy, at least under standardized in vitro conditions. Preferential mineralization of simple organic substrates in the rich fen and complex compounds in the poor fen was not observed. Similarly, no preference was given to “native” organic matter extracts derived from each fen, with microbial communities opting for the most bioavailable substrate. This study suggests that soil bacteria and fungi might be able to respond relatively rapidly to shifts in vegetation communities and subsequent changes in the quality of carbon substrate additions to peatlands associated with environmental and climatic change.

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Influence of moisture and freeze–thaw on leaf microbial community dynamics

Canadian Journal of Forest Research ◽

10.1139/x09-199 ◽

2010 ◽

Vol 40 (2) ◽

pp. 394-400 ◽

Cited By ~ 1

Author(s):

C. Corrigan ◽

M. Oelbermann

Keyword(s):

Organic Matter ◽

Community Structure ◽

Microbial Community ◽

Sugar Maple ◽

Community Dynamics ◽

Nitrogen Concentration ◽

Fagus Grandifolia ◽

Nutrient Inputs ◽

Freezing And Thawing ◽

Freeze Thaw

In forest ecosystems, litterfall that collects in trapping devices, to quantify organic matter and nutrient inputs, is exposed to periods of wetting, drying, freezing, and thawing. These fluctuating environmental conditions may influence the microbial community structure inhabiting the leaves and may result in the loss of mobile nutrients, leading to an underestimation of actual organic matter and nutrient inputs. The objectives of this study were to evaluate the influence of (i) different quantities of moisture (LOW = 30 mm, MED = 60 mm, HI = 100 mm) and (ii) freeze–thaw (FT) on leaf (sugar maple ( Acer saccharum Marsh.), American basswood ( Tilia americana L.), and American beech ( Fagus grandifolia Ehrh.)) microbial activity and community structure. There was a significantly greater (p < 0.05) CO2 production rate in LOW and FT treatments for sugar maple and beech, and in HI and FT treatments for basswood. A similar trend occurred for leaf nitrogen concentration but not for carbon (C). Utilization of C substrates was up to 10% greater in the FT treatments. Principal components analysis on the activity of C source utilization showed a distinct clustering between leaf species and between treatments following a pattern similar to that of microbial respiration. Results from this study suggested that the collection of litter should take place more frequently during seasons when frost is imminent.

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Microbial dynamics in a High-Arctic glacier forefield: a combined field, laboratory, and modelling approach

10.5194/bg-2016-52 ◽

2016 ◽

Author(s):

James A. Bradley ◽

Sandra Arndt ◽

Marie Šabacká ◽

Liane G. Benning ◽

Gary L. Barker ◽

...

Keyword(s):

Microbial Community ◽

Numerical Model ◽

Microbial Communities ◽

Community Dynamics ◽

Heterotrophic Bacteria ◽

High Arctic ◽

Soil Development ◽

Arctic Soils ◽

Field Laboratory ◽

Modelling Approach

Abstract. Modelling the development of soils in glacier forefields is necessary in order to assess how microbial and geochemical processes interact and shape soil development in response to glacier retreat. Furthermore, such models can help us predict microbial growth and the fate of Arctic soils in an increasingly ice-free future. Here, for the first time, we combined field sampling with laboratory analyses and numerical modelling to investigate microbial community dynamics in oligotrophic proglacial soils in Svalbard. We measured low bacterial growth rates and growth efficiencies (relative to estimates from Alpine glacier forefields), and high sensitivity to soil temperature (relative to temperate soils). We used these laboratory measurements to inform parameter values in a new numerical model and significantly refined predictions of microbial and biogeochemical dynamics of soil development over a period of roughly 120 years. The model predicted the observed accumulation of autotrophic and heterotrophic biomass. Genomic data indicated that initial microbial communities were dominated by bacteria derived from the subglacial environment, whereas older soils hosted a mixed community of autotrophic and heterotrophic bacteria. This finding was validated by the numerical model, which showed that active microbial communities play key roles in fixing and recycling carbon and nutrients. We also demonstrated the role of allochthonous carbon and microbial necromass in sustaining a pool of organic material, despite high heterotrophic activity in older soils. This combined field, laboratory and modelling approach demonstrates the value of integrated model-data studies to understand and quantify the functioning of the microbial community in an emerging High-Arctic soil ecosystem.

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RNA-seq provides molecular insights into interaction modification in simplified microbial community

Access Microbiology ◽

10.1099/acmi.ac2020.po0801 ◽

2020 ◽

Vol 2 (7A) ◽

Author(s):

Frederik De Boever ◽

Philippe Potin ◽

David Green

Keyword(s):

Microbial Community ◽

Community Dynamics ◽

Heterotrophic Bacteria ◽

Context Dependency ◽

Emergent Properties ◽

Interspecies Interactions ◽

Transcriptional Responses ◽

Nutrient Analysis ◽

Primary Producer ◽

The Stability

A major challenge in microbial ecology is to understand the stability of interspecies interactions when progressing from pairs of interacting species to multispecies interaction networks. A lack of direct evidence, and a conceptual framework to explore how direct and indirect effects shape cellular responses in species-rich networks has hindered progress in our understanding of these combined effects. Here we aimed to investigate whether higher-order interactions shape community dynamics and transcriptional profiles of all interacting partners in a simplified microbial community that includes a primary producer (Nannochloropsis oceanica CCAP849/10) and two heterotrophic bacteria (Marinobacter sp. FDB33 and Alteromonas sp. FDB36). By combining co-cultivation assays, quantification of absolute abundances, nutrient analysis, and simultaneous RNA-sequencing, we reveal genome-wide transcriptional responses in all binary co-cultivation partners and show that the third partner can profoundly alter binary interactions at the phenotypic and transcription level. Our study demonstrates the context-dependency of binary interactions, whereby environmental conditions and the presence of specific organisms can affect the cellular physiology of the interacting partners and ultimately the stability of the community. Furthermore, our approach provides a powerful tool for probing the molecular basis of emergent properties in more complex systems.

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Changes in Microbial Community Phylogeny and Metabolic Activity Along the Water Column Uncouple at Near Sediment Aphotic Layers in Fjords

10.21203/rs.3.rs-334470/v1 ◽

2021 ◽

Author(s):

Sven P. Tobias-Hünefeldt ◽

Stephen R. Wing ◽

Federico Baltar ◽

Sergio E. Morales

Keyword(s):

Organic Matter ◽

Microbial Community ◽

Water Column ◽

Microbial Activity ◽

Community Composition ◽

Microbial Community Composition ◽

Leucine Incorporation ◽

Metabolic Potential ◽

Near Surface ◽

Potential Activity

Abstract Fjords are semi-enclosed marine systems with unique physical conditions that influence microbial community composition and structure. Pronounced organic matter and physical condition gradients within fjords provide a natural laboratory for the study of changes in microbial phylogeny and metabolic potential in response to environmental conditions. Photosynthetic production in euphotic zones sustains deeper aphotic microbial activity via organic matter sinking, augmented by large terrestrial inputs. We profiled microbial functional potential (Biolog Ecoplates), bacterial abundance, heterotrophic production (3H-Leucine incorporation), and prokaryotic/eukaryotic community composition (16S and 18S rRNA amplicon gene sequencing) to link metabolic potential, activity, and community composition to known community drivers. Similar factors shaped metabolic potential, activity and community (prokaryotic and eukaryotic) composition across surface/near surface sites. However, increased metabolic diversity at near bottom (aphotic) sites reflected an organic matter influence from sediments. Photosynthetically produced particulate organic matter shaped the upper water column community composition and metabolic potential. In contrast, microbial activity at deeper aphotic waters were strongly influenced by other organic matter imput than sinking marine snow (e.g. sediment resuspension of benthic organic matter, remineralisation of terrestrially derived organic matter, etc.), severing the link between phylogeny and metabolic potential. Taken together, different organic matter sources shape microbial activity, but not community composition, in New Zealand fjords.

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Performance and microbial community of the CANON process in a sequencing batch membrane bioreactor with elevated COD/N ratios

Water Science & Technology ◽

10.2166/wst.2020.089 ◽

2020 ◽

Vol 81 (1) ◽

pp. 138-147

Author(s):

Xiaoling Zhang ◽

Xincong Liu ◽

Meng Zhang

Keyword(s):

Organic Matter ◽

Microbial Community ◽

Nitrogen Removal ◽

Membrane Bioreactor ◽

Ammonia Oxidation ◽

Heterotrophic Bacteria ◽

Removal Rate ◽

Ammonia Oxidizing Bacteria ◽

Anaerobic Ammonia Oxidation ◽

Canon Process

Abstract In this study, the effects of elevated chemical oxygen demand/nitrogen (COD/N) ratios on nitrogen removal, production and composition of the extracellular polymer substances (EPS) and microbial community of a completely autotrophic nitrogen removal via nitrite (CANON) process were studied in a sequencing batch membrane bioreactor (SBMBR). The whole experiment was divided into two stages: the CANON stage (without organic matter in influent) and the simultaneous partial nitrification, anaerobic ammonia oxidation and denitrification (SNAD) stage (with organic matter in influent). When the inflow ammonia nitrogen was 420 mg/L and the COD/N ratio was no higher than 0.8, the addition of COD was helpful to the CANON process; the total nitrogen removal efficiency (TNE) was improved from approximately 65% to more than 75%, and the nitrogen removal rate (NRR) was improved from approximately 0.255 kgN/(m3·d) to approximately 0.278 kgN/(m3•d), while the TNE decreased to 60%, and the NRR decreased to 0.236 kgN/(m3•d) when the COD/N ratio was elevated to 1.0. For the EPS, the amounts of soluble EPS (SEPS) and loosely bound EPS (LB-EPS) were both higher in the CANON stage than in the SNAD stage, while the amount of tightly bound EPS (TB-EPS) in the SNAD stage was significantly higher due to the proliferation of heterotrophic bacteria. The metagenome sequencing technique was used to analyse the microbial community in the SBMBR. The results showed that the addition of COD altered the structure of the bacterial community in the SBMBR. The amounts of Candidatus ‘Anammoxoglobus’ of anaerobic ammonia oxidation bacteria (AAOB) and Nitrosomonas of ammonia oxidizing bacteria (AOB) both decreased significantly, and Nitrospira of nitrite oxidizing bacteria (NOB) was always in the reactor, although the amount changed slightly. A proliferation of denitrifiers related to the genera of Thauera, Dokdonella and Azospira was found in the SBMBR.

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Metabolic tuning of a stable microbial community in the surface oligotrophic Indian Ocean revealed by integrated meta-omics

Marine Life Science & Technology ◽

10.1007/s42995-021-00119-6 ◽

2022 ◽

Author(s):

Zhang-Xian Xie ◽

Ke-Qiang Yan ◽

Ling-Fen Kong ◽

Ying-Bao Gai ◽

Tao Jin ◽

...

Keyword(s):

Microbial Community ◽

Indian Ocean ◽

Microbial Communities ◽

Fine Tuning ◽

Metabolic Potential ◽

Environmental Forcing ◽

Metabolic Functions ◽

Microbial Response ◽

The Stability ◽

And Function

AbstractUnderstanding the mechanisms, structuring microbial communities in oligotrophic ocean surface waters remains a major ecological endeavor. Functional redundancy and metabolic tuning are two mechanisms that have been proposed to shape microbial response to environmental forcing. However, little is known about their roles in the oligotrophic surface ocean due to less integrative characterization of community taxonomy and function. Here, we applied an integrated meta-omics-based approach, from genes to proteins, to investigate the microbial community of the oligotrophic northern Indian Ocean. Insignificant spatial variabilities of both genomic and proteomic compositions indicated a stable microbial community that was dominated by Prochlorococcus, Synechococcus, and SAR11. However, fine tuning of some metabolic functions that are mainly driven by salinity and temperature was observed. Intriguingly, a tuning divergence occurred between metabolic potential and activity in response to different environmental perturbations. Our results indicate that metabolic tuning is an important mechanism for sustaining the stability of microbial communities in oligotrophic oceans. In addition, integrated meta-omics provides a powerful tool to comprehensively understand microbial behavior and function in the ocean.

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