Microbial Ecology

Fungal Community Composition and Potential Depth-Related Driving Factors Impacting Distribution Pattern and Trophic Modes from Epi- to Abyssopelagic Zones of the Western Pacific Ocean Abstract Fungi play an important role in cycling organic matter and nutrients in marine ecosystems. However, the distribution of fungal communities in the ocean, especially the vertical distribution along depth in the water column, remained poorly understood. Here, we assess the depth-related distribution pattern of fungal communities along the water column from epi- to abyssopelagic zones of the Western Pacific Ocean using internal transcribed spacer 2 (ITS2) metabarcoding. Majority of the assigned OTUs were affiliated to Ascomycota, followed by three other minor phyla (Basidiomycota, Chytridiomycota, and Mucoromycota). The epipelagic zone harbored a higher OTU richness with distinct fungal communities as compared with meso-, bathy-, and abyssopelagic zones. Across the whole water column, depth appears as a key parameter for both fungal α- and β-diversity. However, when the dataset was split into the upper (5–500 m) and deeper (below 500 m) layers, no significant correlation was observed between depth and community compositions. In the upper layer, temperature and dissolved oxygen were recognized as the primary environmental factors shaping fungal α- and β- diversity. By parsing fungal OTUs into ecological categories, multi-trophic mode of nutrition was found to be more prevalent with increasing depth, suggesting a potential adaptation to the extreme conditions of the deep sea. This study provides new and meaningful information on the depth-stratified fungal diversity, community structure, and putative ecological roles in the open sea.

Bacterial Community Composition and Diversity Respond to Nutrient Amendment but Not Warming in a Maritime Antarctic Soil Abstract A resumption of climate warming in maritime Antarctica, arising from continued greenhouse gas emissions to the atmosphere, is predicted to lead to further expansions of plant populations across the region, with consequent increases in nutrient inputs to soils. Here, we test the main and interactive effects of warming, applied with open top chambers (OTCs), and nutrient amendment with tryptic soy broth (TSB), an artificial growth substrate, on bacterial community composition and diversity using Illumina sequencing of 16S rRNA genes in soil from a field experiment in the southern maritime Antarctic. Substantial effects of TSB application on bacterial communities were identified after 49 months, including reduced diversity, altered phylogenetic community assembly processes, increased Proteobacteria-to-Acidobacteria ratios and significant divergence in community composition, notably increases in the relative abundances of the gram-positive genera Arthrobacter, Paeniglutamicibacter and Planococcus. Contrary to previous observations from other maritime Antarctic field warming experiments, we recorded no effects of warming with OTCs, or interactive effects of OTCs and TSB application, on bacterial community composition or diversity. Based on these findings, we conclude that further warming of the maritime Antarctic is unlikely to influence soil bacterial community composition or diversity directly, but that increased nutrient inputs arising from enhanced plant growth across the region may affect the composition of soil bacterial communities, with possible effects on ecosystem productivity.

Characterization of Bacterial Communities in Breeding Waters of Anopheles darlingi in Manaus in the Amazon Basin Malaria-Endemic Area Abstract The microbiota in mosquito breeding waters can affect ovipositing mosquitoes, have effects on larval development, and can modify adult mosquito-gut bacterial composition. This, in turn, can affect transmission of human pathogens such as malaria parasites. Here, we explore the microbiota of four breeding sites for Anopheles darlingi, the most important malaria vector in Latin America. The sites are located in Manaus in the Amazon basin in Brazil, an area of active malaria transmission. Using 16S rRNA gene sequencing by MiSeq, we found that all sites were dominated by Proteobacteria and Firmicutes and that 94% of the total number of reads belonged to 36 operational taxonomic units (OTUs) identified in all sites. Of these, the most common OTUs belonged to Escherichia/Shigella, Staphylococcus, and Pseudomonas. Of the remaining 6% of the reads, the OTUs found to differentiate between the four sites belonged to the orders Burkholderiales, Actinomycetales, and Clostridiales. We conclude that An. darlingi can develop in breeding waters with different surface-water bacteria, but that the common microbiota found in all breeding sites might indicate or contribute to a suitable habitat for this important malaria vector.

Community Ecology of Deinococcus in Irradiated Soil Abstract Deinococcus is a genus of soil bacteria known for radiation resistance. However, the effects of radiation exposure on its community structure are unknown. We exposed soil to three levels of gamma radiation, 0.1 kGy/h (low), 1 kGy/h (medium), and 3 kGy/h (high), once a week for 6 weeks and then extracted soil DNA for 16S rRNA amplicon sequencing. We found the following: (1) Increasing radiation dose produced a major increase in relative abundance of Deinococcus, reaching ~ 80% of reads at the highest doses. Differing abundances of the various Deinococcus species in relation to exposure levels indicate distinct "radiation niches." At 3 kGy/h, a single OTU identified as D. ficus overwhelmingly dominated the mesocosms. (2) Corresponding published genome data show that the dominant species at 3 kGy/h, D. ficus, has a larger and more complex genome than other Deinococcus species with a greater proportion of genes related to DNA and nucleotide metabolism, cell wall, membrane, and envelope biogenesis as well as more cell cycle control, cell division, and chromosome partitioning-related genes. Deinococcus ficus also has a higher guanine–cytosine ratio than most other Deinococcus. These features may be linked to genome stability and may explain its greater abundance in this apparently competitive system, under high-radiation exposures. (3) Genomic analysis suggests that Deinococcus, including D. ficus, are capable of utilizing diverse carbon sources derived from both microbial cells killed by the radiation (including C5–C12-containing compounds, like arabinose, lactose, N-acetyl-d-glucosamine) and plant-derived organic matter in the soil (e.g., cellulose and hemicellulose). (4) Overall, based on its metagenome, even the most highly irradiated (3 kGy/h) soil possesses a wide range of the activities necessary for a functional soil system. Future studies may consider the resilience and sustainability of such soils in a high-radiation environment.

Functional Response of MBR Microbial Consortia to Substrate Stress as Revealed by Metaproteomics Abstract Bacterial consortia have a primary role in the biological degradations occurring in activated sludge for wastewater treatment, for their capacities to metabolize the polluting matter. Therefore, the knowledge of the main metabolic pathways for the degradation of pollutants becomes critical for a correct design and operation of wastewater treatment plants. The metabolic activity of the different bacterial groups in activated sludge is commonly investigated through respirometry. Furthermore, in the last years, the development of "omic" approaches has offered more opportunities to integrate or substitute the conventional microbiological assays and to deeply understand the taxonomy and dynamics of complex microbial consortia. In the present work, an experimental membrane bioreactor (MBR) was set up and operated for the treatment of municipal wastewater, and the effects of a sudden decrease of the organic supply on the activated sludge were investigated. Both respirometric and metaproteomic approaches revealed a resistance of autotrophic bacteria to the substrate stress, and particularly of nitrifying bacteria. Furthermore, metaproteomics allowed the identification of the taxonomy of the microbial consortium based on its protein expression, unveiling the prevalence of Sorangium and Nitrosomonas genera both before and after the organic load decrease. Moreover, it confirmed the results obtained through respirometry and revealed a general expression of proteins involved in metabolism and transport of nitrogen, or belonging to nitrifying species like Nitrosomonas europeae, Nitrosomonas sp. AL212, or Nitrospira defluvii.

Edaphic Factors Influence the Distribution of Arbuscular Mycorrhizal Fungi Along an Altitudinal Gradient of a Tropical Mountain Abstract Changes in relief in montane areas, with increasing altitude, provide different biotic and abiotic conditions, acting on the species of arbuscular mycorrhizal fungi (AMF). The objective of this work was to determine the influence of altitude, edaphic factors, and vegetation on the AMF species in a mountainous area. The list of AMF species was obtained from morphological identification of the spores, with 72 species recovered from field samples and trap cultures. Lower levels of Shannon's diversity occurred only at lower altitude; however, there was no difference in AMF richness. The structure of the AMF assembly between the two highest altitudes was similar and differed in relation to the lower altitude. There was variation in the distribution of AMF species, which was related to soil texture and chemical factors along the altitude gradient. Some species, genera, and families were indicative of a certain altitude, showing the preference of fungi for certain environmental conditions, which may aid in decisions to conserve montane ecosystems.

A Physiological and Genomic Comparison of Nitrosomonas Cluster 6a and 7 Ammonia-Oxidizing Bacteria Abstract Ammonia-oxidizing bacteria (AOB) within the genus Nitrosomonas perform the first step in nitrification, ammonia oxidation, and are found in diverse aquatic and terrestrial environments. Nitrosomonas AOB were grouped into six defined clusters, which correlate with physiological characteristics that contribute to adaptations to a variety of abiotic environmental factors. A fundamental physiological trait differentiating Nitrosomonas AOB is the adaptation to either low (cluster 6a) or high (cluster 7) ammonium concentrations. Here, we present physiological growth studies and genome analysis of Nitrosomonas cluster 6a and 7 AOB. Cluster 6a AOB displayed maximum growth rates at ≤ 1 mM ammonium, while cluster 7 AOB had maximum growth rates at ≥ 5 mM ammonium. In addition, cluster 7 AOB were more tolerant of high initial ammonium and nitrite concentrations than cluster 6a AOB. Cluster 6a AOB were completely inhibited by an initial nitrite concentration of 5 mM. Genomic comparisons were used to link genomic traits to observed physiological adaptations. Cluster 7 AOB encode a suite of genes related to nitrogen oxide detoxification and multiple terminal oxidases, which are absent in cluster 6a AOB. Cluster 6a AOB possess two distinct forms of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and select species encode genes for hydrogen or urea utilization. Several, but not all, cluster 6a AOB can utilize urea as a source of ammonium. Hence, although Nitrosomonas cluster 6a and 7 AOB have the capacity to fulfill the same functional role in microbial communities, i.e., ammonia oxidation, differentiating species-specific and cluster-conserved adaptations is crucial in understanding how AOB community succession can affect overall ecosystem function.

Impacts of Freshwater and Seawater Mixing on the Production and Decay of Virioplankton in a Subtropical Estuary Abstract Virioplankton is an important component of the aquatic ecosystem and plays multiple ecological and biogeochemical roles. Although the spatial and temporal distributions and dynamics of virioplankton have been well investigated in riverine and marine environments, little is known about the dynamics and environmental controlling mechanisms of virioplankton in estuaries. In this study, viral abundance, production and decay were examined in the Pearl River Estuary (PRE), one of the largest estuaries in China. The influences of freshwater and seawater mixing on viral ecological dynamics were evaluated with several cross-transplant experiments. In PRE, viral abundance, production and decay rates varied from 2.72 ± 0.09 to 27.5 ± 1.07 × 106 viruses ml−1, 7.98 ± 2.33 to 16.27 ± 2.85% h−1 and 0.80 ± 0.23 to 3.74 ± 0.98% h−1, respectively. When the riverine and marine microbial community were transferred into simulated brackish water, viral production rates were markedly inhibited by 83.8% and 47.3%, respectively. The decay of riverine and marine virioplankton was inhibited by 21.1% and 34.2%, respectively, in simulated brackish water. These results indicate change of estuarine environmental factors significantly alters the dynamics of riverine and marine virioplankton. In addition, the effects of mixing on viral production and decay differed between high- and low-fluorescence viruses. High-fluorescence viruses seemed more resistant to decay than low-fluorescence viruses, whereas the production of marine low-fluorescence viruses seemed more resistant to inhibition than that of marine high-fluorescence viruses. Together, these results provide new insights into the ecological dynamics of virioplankton in estuarine environments.

Time-Dependent Hormetic Response of Soil Alkaline Phosphatase Induced by Cd and the Association with Bacterial Community Composition Abstract Hormetic dose-response that involved Cd in soils is increasingly paid attentions for risk assessment of Cd toxicity, but insufficient studies were conducted to define the temporary modification of soil enzyme and the potential microbial responses. The present study chooses soil alkaline phosphatase (ALP) as endpoint to uncover the time-dependent hormetic responses to low doses of Cd and its association with bacterial community composition. The results showed that addition of 0.01–3.0 mg kg−1 Cd significantly increased ALP's activities with maximum stimulatory magnitude of 11.4–27.2%, indicating a typical hormesis. The response started at 12 h after Cd addition and maintained about 24 h. This demonstrated that the hormetic response is time-dependent and transient. Changes of soil bacterial community composition showed that, at 6 h, relative abundances (RAs) of Proteobacteria and Firmicutes at phylum and Pontibacter, Bacillaceae-Bacillus, Bacillaceae1-Bacillus, and Paenisporosarcina at genus significantly correlated with ALP's activities at 12–36 h (P < 0.05). This suggests that soil bacteria likely showed an earlier response to Cd and potentially contributes to the subsequent soil enzyme's hormesis. In addition, it was found that Gram-negative bacteria other than Gram-positive bacteria are prone to exhibiting a hormetic response under Cd stress. Our findings provide much insight into ecotoxicological risk assessment for soil Cd pollution.

A Polyphasic Approach for Assessing Eco-System Connectivity Demonstrates that Perturbation Remodels Network Architecture in Soil Microcosms Abstract Network analysis was used to show changes in network attributes by analyzing the relations among the main soil microbial groups in a potted tomato soil inoculated with arbuscular mycorrhizal fungus, treated with low doses of Mentha spicata essential oil, or both, and then exposed to tenfold higher oil addition (stress pulse). Pretreatments were chosen since they can induce changes in the composition of the microbial community. Cellular phospholipid fatty acids (PLFAs) and the activity of six soil enzymes, mainly involved in the N-cycle were measured. Networks were constructed based on correlated changes in PLFA abundances. The values of all parameters were significantly different from those of random networks indicating modular architecture. Networks ranked from the lowest to highest modularity: control, non-pretreated and stressed, inoculated and stressed, oil treated and stressed, inoculated and treated with oil and stressed. The high values of network density and 1st/2nd eigenvalue ratio are related to arylamidase activity while N-acetyl-glucosaminidase, acid phosphomoesterase, and asparaginase activities related to high values of the clustering coefficient index. We concluded that modularity may be an efficient indicator of changes in the network of interactions among the members of the soil microbial community and the modular structure of the network may be related to the activity of specific enzymes. Communities that were stressed without a pretreatment were relatively resistant but prone to sudden transition towards instability, while oil or inoculation pretreatments gave networks which could be considered adaptable and susceptible to gradual change.