Posts Tagged 'fungi'

Stimulation of N2O emission via bacterial denitrification driven by acidification in estuarine sediments

Ocean acidification in nitrogen-enriched estuaries has raised global concerns. For decades, biotic and abiotic denitrification in estuarine sediments have been regarded as the major ways to remove reactive nitrogen, but they occur at the expense of releasing greenhouse gas nitrous oxide (N2O). However, how these pathways respond to acidification remains poorly understood. Here we performed a N2O isotopocules analysis coupled with respiration inhibition and molecular approaches to investigate the impacts of acidification on bacterial, fungal, and chemo-denitrification, as well as N2O emission, in estuarine sediments through a series of anoxic incubations. Results showed that acidification stimulated N2O release from sediments, which was mainly mediated by the activity of bacterial denitrifiers, while in neutral environments, N2O production was dominated by fungi. We also found that the contribution of chemo-denitrification to N2O production cannot be ignored, but was not significantly affected by acidification. The mechanistic investigation further demonstrated that acidification changed the keystone taxa of sedimentary denitrifiers from N2O-reducing to N2O-producing ones, and reduced microbial electron transfer efficiency during denitrification. These findings provide novel insights into how acidification stimulates N2O emission and modulates its pathways in estuarine sediments, and how it may contribute to the acceleration of global climate change in the Anthropocene.

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Bacterial communities are more sensitive to ocean acidification than fungal communities in estuarine sediments

Ocean acidification (OA) in estuaries is becoming a global concern, and may affect microbial characteristics in estuarine sediments. Bacterial communities in response to acidification in this habitat have been well discussed; however, knowledge about how fungal communities respond to OA remains poorly understood. Here, we explored the effects of acidification on bacterial and fungal activities, structures and functions in estuarine sediments during a 50-day incubation experiment. Under acidified conditions, activities of three extracellular enzymes related to nutrient cycling were inhibited and basal respiration rates were decreased. Acidification significantly altered bacterial communities and their interactions, while weak alkalization had a minor impact on fungal communities. We distinguished pH-sensitive/tolerant bacteria and fungi in estuarine sediments, and found that only pH-sensitive/tolerant bacteria had strong correlations with sediment basal respiration activity. FUNGuild analysis indicated that animal pathogen abundances in sediment were greatly increased by acidification, while plant pathogens were unaffected. High-throughput quantitative PCR-based SmartChip analysis suggested that the nutrient cycling-related multifunctionality of sediments was reduced under acidified conditions. Most functional genes associated with nutrient cycling were identified in bacterial communities and their relative abundances were decreased by acidification. These new findings highlight that acidification in estuarine regions affects bacterial and fungal communities differently, increases potential pathogens and disrupts bacteria-mediated nutrient cycling.

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High-resolution time-series reveals seasonal patterns of planktonic fungi at a temperate coastal ocean site (Beaufort, North Carolina, USA)

There is a growing awareness of the ecological and biogeochemical importance of fungi in coastal marine systems, while highly diverse fungi have been discovered in these marine systems, still little is known about their seasonality and associated drivers in coastal waters. Here, we examined fungal communities over three years of weekly samples at a dynamic, temperate coastal site (Piver’s Island Coastal Observatory (PICO), Beaufort NC USA). Fungal 18S rRNA gene abundance, OTU richness and Shannon’s diversity exhibited prominent seasonality. Fungi 18S rRNA gene copies peak in abundance during the summer and fall, with positive correlations with chlorophyll a, SiO4 and oxygen saturation. Diversity (measured using Internal Transcribed Spacer: ITS libraries) was highest during winter and lowest during summer; it was linked to temperature, pH, chlorophyll a, insolation, salinity, and DIC. Fungal community ITS libraries were dominated throughout the year by Ascomycota with contributions from Basidiomycota, Chytridiomycota and Mucoromycotina, with seasonal patterns linked to water temperature, light, and the carbonate system. Network analysis revealed that while co-occurrence and exclusion existed within fungal network, exclusion dominated the fungi and phytoplankton network, in contrast with reported pathogenic and nutritional interactions between marine phytoplankton and fungi. Compared with the seasonality of bacterial community in the same samples, the timing, extent and associated environmental variables for fungi community are unique. These results highlighted the fungal seasonal dynamics in coastal water and improve our understanding of the ecology of planktonic fungi.

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Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: Evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak

The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidification on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2mesocosms (~ 760 μatm) and those exposed to present-day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients. Furthermore, based on our investigations, the elevated CO2 did not affect the intraspecific diversity of the most common mesozooplankter, the calanoid copepod Pseudocalanus acuspes. Nevertheless, accompanying studies found temporary effects attributed to a raise in CO2. Differences in taxa composition between the CO2 treatments could, however, only be observed in a specific period of the experiment. Based on our genetic investigations, no compositional long-term shifts of the plankton communities exposed to elevated CO2 conditions were observed. Thus, we conclude that the compositions of planktonic communities, especially those in coastal areas, remain rather unaffected by increased CO2.

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Impacts of a reduction in seawater pH mimicking ocean acidification on the structure and diversity of mycoplankton communities

Increases in atmospheric carbon dioxide (CO2) change ocean chemistry, as dissolved CO2 leads to a reduction in the seawater pH. Many marine taxa have been shown to be affected by ocean acidification; however, information on marine fungi is lacking. We analyzed the effect of pH on mycoplankton communities. The pH of microcosms was adjusted to a value mimicking the predicted ocean acidification in the near future. Fungal communities were analyzed using a double-marker gene approach, allowing a more detailed analysis of their response using 454 pyrosequencing. Mycoplankton communities in microcosms with in situ and adjusted water pH values differed significantly in terms of structure and diversity. The differences were mainly abundance shifts among the dominant taxa, rather than the exclusion of fungal groups. A sensitivity to lower pH values was reported for several groups across the fungal kingdom and was not phylogenetically conserved. Some of the fungal species that dominated the communities of microcosms with a lower pH were known pathogenic fungi. With the increasing awareness of the significant role fungi play in marine systems, including performing a diverse range of symbiotic activities, our results highlight the importance of including fungi in further research projects studying and modeling biotic responses to the predicted ocean acidification.

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Sponge biomass and bioerosion rates increase under ocean warming and acidification

The combination of ocean warming and acidification as a result of increasing atmospheric carbon dioxide (CO2) is considered to be a significant threat to calcifying organisms and their activities on coral reefs. How these global changes impact the important roles of decalcifying organisms (bioeroders) in the regulation of carbonate budgets, however, is less understood. To address this important question, the effects of a range of past, present and future CO2 emission scenarios (temperature + acidification) on the excavating sponge Cliona orientalis Thiele, 1900 were explored over twelve weeks in early summer on the southern Great Barrier Reef. C. orientalis is a widely distributed bioeroder on many reefs, and hosts symbiotic dinoflagellates of the genus Symbiodinium. Our results showed that biomass production and bioerosion rates of C. orientalis were similar under a pre-industrial scenario and a present day (control) scenario. Symbiodinium population density in the sponge tissue was the highest under the pre-industrial scenario, and decreased towards the two future scenarios with sponge replicates under the ʻbusiness-as-usualʼ CO2 emission scenario exhibiting strong bleaching. Despite these changes, biomass production rates and the ability of the sponge to erode coral carbonate materials both increased under the future scenarios. Our study suggests that C. orientalis will likely grow faster and have higher bioerosion rates in a high CO2 future than at present, even with significant bleaching. Assuming that our findings hold for excavating sponges in general, increased sponge biomass coupled with accelerated bioerosion may push coral reefs towards net erosion and negative carbonate budgets in the future.

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Ocean acidification effects on marine microbial communities

Anthropogenic CO2 emissions are causing an acidification of the world’s oceans. The consequences for marine organisms and especially heterotrophic bacteria remain under debate, and almost nothing is known concerning marine fungi. Both microbial groups are important players in organic matter decomposition and nutrient cycling, and their pH tolerance is known to be broad in relation to the predicted acidification. So far, ocean acidification effects on marine bacterial communities have mainly been investigated in large-scale mesocosm studies. In these systems, indirect effects mediated through complex food web interactions come into play. Until now, these experiments were not carried out in sufficient replication. In this thesis, we chose an alternative approach and investigated bacterial and fungal communities in highly replicated microcosm experiments (1-1.6 L). The duration of the experiments was four weeks. We incubated the natural microbial community from Helgoland Roads (North Sea) at in situ seawater pH, pH 7.82 and pH 7.67. These pH levels represent the present-day situation and acidification at atmospheric CO2 of 700 or 1000 ppm, projected for the southern North Sea for the year 2100. For the bacterial community, different dilution approaches were used to select for different ecological groups. Seasonality was accounted for by repeating the experiment four times (spring, summer, autumn, winter). In a second experiment repeated in two consecutive years, we investigated direct pH effects on marine fungal communities. We additionally isolated marine yeasts and identified them by Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and partial sequencing of the large subunit (LSU) rRNA gene. To reveal changes in community structure, we applied the culture-independent fingerprint method automated ribosomal intergenic spacer analysis (ARISA) for both bacteria and fungi. Bacterial communities were furthermore analyzed by 16S ribosomal amplicon pyrosequencing. Abundances were determined by flow cytometry (bacteria) and colony forming unit counts (fungi). To be able to interpret results comprehensively, we determined the natural variability of the carbonate system at Helgoland Roads over a yearly cycle. We found that from September 2010 to September 2011, pH at Helgoland Roads ranged from 8.06 to 8.43, corresponding to partial pressures of carbon dioxide (pCO2) of 215-526 µatm. The acidification predicted for the year 2100 consequently represents a strong perturbation of the system. Bacterial communities developing in the microcosms were primarily influenced by season and dilution, demonstrating that diverse communities had been generated. We predominantly found pH-dependent shifts in bacterial community structure already at pH 7.82. Groups involved in these shifts were different members of Gammaproteobacteria, Flavobacteriaceae, Rhodobacteraceae, Campylobacteraceae and further less abundant groups. While Rhodobacteraceae were consistently less characteristic for reduced pH, Campylobacteraceae profited from pH reduction. For most other bacterial groups however, pH effects were context-dependent, i.e. dependent on season, dilution or an interaction of effects. Regarding bacterial abundance, no pH effect was found. Fungal community structure was significantly different between both years of the experiment, hinting at inter-annual variability. Shifts in response to pH occurred predominantly only at pH 7.67. In contrast, a strong pH effect was observed on fungal abundance. In comparison to in situ pH, fungal numbers were on average 9 times higher at pH 7.82 and 34 times higher at pH 7.67. Concerning marine yeasts, Leucosporidium scottii, Rhodotorula mucilaginosa and related species, as well as Cryptococcus sp. and Debaromyces hansenii reacted positively to low pH. Our findings demonstrate that already small reductions in pH have direct effects on both bacterial and fungal communities. A tipping point for community shifts appears to be reached earlier for bacteria than for fungi. Regarding bacteria and yeasts, both naturally abundant groups and rare species were affected by pH reductions. The strong increase in fungal numbers at reduced pH suggests that with ocean acidification, marine fungi may reach higher importance in marine biogeochemical cycles and as infectious agents. Using a microcosm approach, a robust analysis of direct ocean acidification effects on marine bacterial and fungal communities was accomplished. Results yield valuable hypotheses to test in future large-scale and long-term studies.

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Marine fungi may benefit from ocean acidification

Recent studies have discussed the consequences of ocean acidification for bacterial processes and diversity. However, the decomposition of complex substrates in marine environments, a key part of the flow of energy in ecosystems, is largely mediated by marine fungi. Although marine fungi have frequently been reported to prefer low pH levels, this group has been neglected in ocean acidification research. We present the first investigation of direct pH effects on marine fungal abundance and community structure. In microcosm experiments repeated in 2 consecutive years, we incubated natural North Sea water for 4 wk at in situ seawater pH (8.10 and 8.26), pH 7.82 and pH 7.67. Fungal abundance was determined by colony forming unit (cfu) counts, and fungal community structure was investigated by the culture-independent fingerprint method Fungal Automated Ribosomal Intergenic Spacer Analysis (F-ARISA). Furthermore, pH at the study site was determined over a yearly cycle. Fungal cfu were on average 9 times higher at pH 7.82 and 34 times higher at pH 7.67 compared to in situ seawater pH, and we observed fungal community shifts predominantly at pH 7.67. Currently, surface seawater pH at Helgoland Roads remains >8.0 throughout the year; thus we cannot exclude that fungal responses may differ in regions regularly experiencing lower pH values. However, our results suggest that under realistic levels of ocean acidification, marine fungi will reach greater importance in marine biogeochemical cycles. The rise of this group of organisms will affect a variety of biotic interactions in the sea.

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Study on the effects of near-future ocean acidification on marine yeasts: a microcosm approach

Marine yeasts play an important role in biodegradation and nutrient cycling and are often associated with marine flora and fauna. They show maximum growth at pH levels lower than present-day seawater pH. Thus, contrary to many other marine organisms, they may actually profit from ocean acidification. Hence, we conducted a microcosm study, incubating natural seawater from the North Sea at present-day pH (8.10) and two near-future pH levels (7.81 and 7.67). Yeasts were isolated from the initial seawater sample and after 2 and 4 weeks of incubation. Isolates were classified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and representative isolates were identified by partial sequencing of the large subunit rRNA gene. From the initial seawater sample, we predominantly isolated a yeast-like filamentous fungus related to Aureobasidium pullulans, Cryptococcus sp., Candida sake, and various cold-adapted yeasts. After incubation, we found more different yeast species at near-future pH levels than at present-day pH. Yeasts reacting to low pH were related to Leucosporidium scottii, Rhodotorula mucilaginosa, Cryptococcus sp., and Debaryomyces hansenii. Our results suggest that these yeasts will benefit from seawater pH reductions and give a first indication that the importance of yeasts will increase in a more acidic ocean.

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