Shifts In Microbial Community Composition Research Articles

Seasonality, rather than estuarine gradient or particle suspension/sinking dynamics, determines estuarine carbon distributions

Estuaries are important components of the global carbon cycle; exchanging carbon between aquatic, atmospheric, and terrestrial environments, representing important loci for blue carbon storage and greenhouse gas emissions. However, how estuarine gradients affect sinking/suspended particles, and dissolved organic matter dynamic interactions remains unexplored. We fractionated suspended/sinking particles to assess and characterise carbon fate differences. We investigated bacterial colonisation (SYBR Green I) and exopolymer concentrations (TEP/CSP) with microscopy staining techniques. C/H/N and dry weight analysis identified particle composition differences. Meanwhile, nutrient and carbon analysis, and excitation and emission matrix evaluations with a subsequent parallel factor (PARAFAC) analysis characterised dissolved organic matter.The lack of clear salinity driven patterns in our study are presumably due to strong mixing forces and high particle heterogeneity along the estuary, with only density differences between suspended and sinking particles. Elbe estuary particles' organic portion is made up of marine-like (sinking) and terrestrial-like (suspended) signatures. Salinity did not have a significant role in microbial degradation and carbon composition, although brackish estuary portions were more biologically active. Indicative of increased degradation rates, leading to decreased greenhouse gas emissions, which are especially relevant for estuaries, with their disproportionate greenhouse gas emissions. Bacterial colonisation decreased seawards, indicative of decreased degradation, and shifts in microbial community composition and functions.Our findings span diverse strands of research, concerning steady carbon contributions from both marine and terrestrial sources, carbon aromaticity, humification index, and bioavailability. Their integration highlights the importance of the Elbe estuary as a model system, providing robust information for future policy decisions affecting dissolved and particulate matter dynamics within the Elbe Estuary.

Unveiling salinity-driven shifts in microbial community composition across compartments of naturally saline inland streams

Riverine environments host diverse microbial communities, exhibiting distinctive assemblies at both microscopic and macroscopic levels. Despite the complexity of microbial life in rivers, the underlying factors that shape the community structure across different compartments remain elusive. Herein, we characterized microbial community composition of biofilm and planktonic (water column) compartments in five naturally saline inland streams and a freshwater stream to examine changes in microbial communities following salinization via sequencing of the microbial 16S rRNA gene. Significant differences in specific conductivity, oxidation–reduction potential, dissolved oxygen, and pH among the sampled streams were measured, as were significant differences in the microbial community composition between the planktonic and biofilm. The bacterial families Bacillaceae, Vicinamibacterceae, and Micrococcaceae were significantly more abundant in the biofilm compartment, while Methylophilaceae, Alcaligenaceae, Spirosomaceae, Burkholderiaceae, and Comamonadaceae were more abundant in the planktonic compartment. In addition, salinity (based on specific conductivity) influenced the microbial community composition in both compartments, with higher sensitivity of the planktonic compartment. Increases in the bacterial families Shewanellaceae, Marinomonadaceae, and Saccharospirillaceae or loss of Anaeromyxobacteraceae could be indicative of increased salinity within inland streams. Our results suggest that monitoring of microbial assemblages of freshwater ecosystems could be used as early warning signs of increased salinization levels.

Shifts in microbial community composition and metabolism correspond with rapid soil carbon accumulation in response to 20 years of simulated nitrogen deposition

Anthropogenic nitrogen (N) deposition and fertilization in boreal forests frequently reduces decomposition and soil respiration and enhances C storage in the topsoil. This enhancement of the C sink can be as strong as the aboveground biomass response to N additions and has implications for the global C cycle, but the mechanisms remain elusive. We hypothesized that this effect would be associated with a shift in the microbial community and its activity, and particularly by fungal taxa reported to be capable of lignin degradation and organic N acquisition. We sampled the organic layer below the intact litter of a Norway spruce (Picea abies (L.) Karst) forest in northern Sweden after 20 years of annual N additions at low (12.5 kg N ha−1 yr−1) and high (50 kg N ha−1 yr−1) rates. We measured microbial biomass using phospholipid fatty-acid analysis (PLFA) and ergosterol measurements and used ITS metagenomics to profile the fungal community of soil and fine-roots. We probed the metabolic activity of the soil community by measuring the activity of extracellular enzymes and evaluated its relationships with the most N responsive soil fungal species. Nitrogen addition decreased the abundance of fungal PLFA markers and changed the fungal community in humus and fine-roots. Specifically, the humus community changed in part due to a shift from Oidiodendron pilicola, Cenococcum geophilum, and Cortinarius caperatus to Tylospora fibrillosa and Russula griseascens. These microbial community changes were associated with decreased activity of Mn-peroxidase and peptidase, and an increase in the activity of C acquiring enzymes. Our results show that the rapid accumulation of C in the humus layer frequently observed in areas with high N deposition is consistent with a shift in microbial metabolism, where decomposition associated with organic N acquisition is downregulated when inorganic N forms are readily available.

Illegal dumping of oil and gas wastewater alters arid soil microbial communities.

The Permian Basin, underlying southeast New Mexico and west Texas, is one of the most productive oil and gas (OG) provinces in the United States. Oil and gas production yields large volumes of wastewater with complex chemistries, and the environmental health risks posed by these OG wastewaters on sensitive desert ecosystems are poorly understood. Starting in November 2017, 39 illegal dumps, as defined by federal and state regulations, of OG wastewater were identified in southeastern New Mexico, releasing ~600,000 L of fluid onto dryland soils. To evaluate the impacts of these releases, we analyzed changes in soil geochemistry and microbial community composition by comparing soils from within OG wastewater dump-affected samples to unaffected zones. We observed significant changes in soil geochemistry for all dump-affected compared with control samples, reflecting the residual salts and hydrocarbons from the OG-wastewater release (e.g., enriched in sodium, chloride, and bromide). Microbial community structure significantly (P < 0.01) differed between dump and control zones, with soils from dump areas having significantly (P < 0.01) lower alpha diversity and differences in phylogenetic composition. Dump-affected soil samples showed an increase in halophilic and halotolerant taxa, including members of the Marinobacteraceae, Halomonadaceae, and Halobacteroidaceae, suggesting that the high salinity of the dumped OG wastewater was exerting a strong selective pressure on microbial community structure. Taxa with high similarity to known hydrocarbon-degrading organisms were also detected in the dump-affected soil samples. Overall, this study demonstrates the potential for OG wastewater exposure to change the geochemistry and microbial community dynamics of arid soils.IMPORTANCEThe long-term environmental health impacts resulting from releases of oil and gas (OG) wastewater, typically brines with varying compositions of ions, hydrocarbons, and other constituents, are understudied. This is especially true for sensitive desert ecosystems, where soil microbes are key primary producers and drivers of nutrient cycling. We found that releases of OG wastewater can lead to shifts in microbial community composition and function toward salt- and hydrocarbon-tolerant taxa that are not typically found in desert soils, thus altering the impacted dryland soil ecosystem. Loss of key microbial taxa, such as those that catalyze organic carbon cycling, increase arid soil fertility, promote plant health, and affect soil moisture retention, could result in cascading effects across the sensitive desert ecosystem. By characterizing environmental changes due to releases of OG wastewater to soils overlying the Permian Basin, we gain further insights into how OG wastewater may alter dryland soil microbial functions and ecosystems.

Monotonic trends of soil microbiomes, metagenomic and metabolomic functioning across ecosystems along water gradients in the Altai region, northwestern China

To investigate microbial communities and their contributions to carbon and nutrient cycling along water gradients can enhance our comprehension of climate change impacts on ecosystem services. Thus, we conducted an assessment of microbial communities, metagenomic functions, and metabolomic profiles within four ecosystems, i.e., desert grassland (DG), shrub-steppe (SS), forest (FO), and marsh (MA) in the Altai region of Xinjiang, China. Our results showed that soil total carbon (TC), total nitrogen, NH4+, and NO3− increased, but pH decreased with soil water gradients. Microbial abundances and richness also increased with soil moisture except the abundances of fungi and protists being lowest in MA. A shift in microbial community composition is evident along the soil moisture gradient, with Proteobacteria, Basidiomycota, and Evosea proliferating but a decline in Actinobacteria and Cercozoa. The β-diversity of microbiomes, metagenomic, and metabolomic functioning were correlated with soil moisture gradients and have significant associations with specific soil factors of TC, NH4+, and pH. Metagenomic functions associated with carbohydrate and DNA metabolisms, as well as phages, prophages, TE, plasmids functions diminished with moisture, whereas the genes involved in nitrogen and potassium metabolism, along with certain biological interactions and environmental information processing functions, demonstrated an augmentation. Additionally, MA harbored the most abundant metabolomics dominated by lipids and lipid-like molecules and organic oxygen compounds, except certain metabolites showing decline trends along water gradients, such as N′-Hydroxymethylnorcotinine and 5-Hydroxyenterolactone. Thus, our study suggests that future ecosystem succession facilitated by changes in rainfall patterns will significantly alter soil microbial taxa, functional potential, and metabolite fractions.

Response of the soil microbial communities to forest ground cover manipulation in a boreal forest

In eastern Canada, boreal forests are locally experiencing a shift between two alternative stable states, productive closed-canopy feather moss (Pleurozium schreberi (Brid.) Mitt.) forests to low-productivity open lichen (Cladonia spp.) woodlands. While this shift has important consequences for ecosystem structure and productivity, little is known about the changes occurring in the diversity and composition of the soil microbial community which may be driven by this process. We evaluated the effects of 10-year moss transplantation on soil microbial communities in an open-lichen woodland. Treatments included: 1) removal of the lichen cover, 2) removal of the lichen cover followed by transplantation of a feather moss cover, 3) a control with the lichen cover kept in place (lichen control), and 4) a natural forest site with a feather moss cover (moss control). We found that changing the forest ground cover has a significant impact on the diversity, composition and function of soil microbial communities. Fungal alpha diversity was more sensitive to changes in lichen and moss cover, compared to bacterial diversity. Soil microbial community composition showed significant differences among all forest ground covers, but with greater similarities between the moss transplantation and control moss treatments. More importantly, changes of forest ground cover significantly affected the structure of microbial communities and fungal functional groups. Moss transplantation significantly increased the relative abundance of the organic nitrogen-scavenging fungal genus, Piloderma. Furthermore, moss transplantation significantly increased the overall relative abundance of ectomycorrhizal fungi and decreased the proportion of ericoid mycorrhizal fungi. Soil moisture and temperature were the main environmental variables associated to the shift in microbial community composition. Our study points out that moss transplantation in open-canopy lichen woodlands contributes to regulate and modify the composition, structure, and function of the soil microbial communities with potential implications for explaining the changes in ecosystem processes associated with these two forest ecosystems.

A dynamics association study of gut barrier and microbiota in hyperuricemia.

The intricate interplay between gut microbiota and hyperuricemia remains a subject of growing interest. However, existing studies only provided snapshots of the gut microbiome at single time points, the temporal dynamics of gut microbiota alterations during hyperuricemia progression and the intricate interplay between the gut barrier and microbiota remain underexplored. Our investigation revealed compelling insights into the dynamic changes in both gut microbiota and intestinal barrier function throughout the course of hyperuricemia. The hyperuricemia mice (HY) were given intragastric administration of adenine and potassium oxalate. Gut microbiota was analyzed by 16S rRNA sequencing at 3, 7, 14, and 21 days after the start of the modeling process. Intestinal permeability as well as LPS, TNF-α, and IL-1β levels were measured at 3, 7, 14, and 21 days. We discovered that shifts in microbial community composition occur prior to the onset of hyperuricemia, key bacterial Bacteroidaceae, Bacteroides, and Blautia exhibited reduced levels, potentially fueling microbial dysbiosis as the disease progresses. During the course of hyperuricemia, the dynamic fluctuations in both uric acid levels and intestinal barrier function was accompanied with the depletion of key beneficial bacteria, including Prevotellaceae, Muribaculum, Parabacteroides, Akkermansia, and Bacteroides, and coincided with an increase in pathogenic bacteria such as Oscillibacter and Ruminiclostridium. This microbial community shift likely contributed to elevated lipopolysaccharide (LPS) and pro-inflammatory cytokine levels, ultimately promoting metabolic inflammation. The decline of Burkholderiaceae and Parasutterella was inversely related to uric acid levels, Conversely, key families Ruminococcaceae, Family_XIII, genera Anaeroplasma exhibited positive correlations with uric acid levels. Akkermansiaceae and Bacteroidaceae demonstrating negative correlations, while LPS-containing microbiota such as Desulfovibrio and Enterorhabdus exhibited positive correlations with intestinal permeability. In summary, this study offers a dynamic perspective on the complex interplay between gut microbiota, uric acid levels, and intestinal barrier function during hyperuricemia progression. Our study suggested that Ruminiclostridium, Bacteroides, Akkermansiaceae, Bilophila, Burkholderiaceae and Parasutterella were the key bacteria that play vital rols in the progress of hyperuricemia and compromised intestinal barrier, which provide a potential avenue for therapeutic interventions in hyperuricemia.

Assessing the Impacts of Lead Corrosion Control on the Microbial Ecology and Abundance of Drinking-Water-Associated Pathogens in a Full-Scale Drinking Water Distribution System.

Increases in phosphate availability in drinking water distribution systems (DWDSs) from the use of phosphate-based corrosion control strategies may result in nutrient and microbial community composition shifts in the DWDS. This study assessed the year-long impacts of full-scale DWDS orthophosphate addition on both the microbial ecology and density of drinking-water-associated pathogens that infect the immunocompromised (DWPIs). Using 16S rRNA gene amplicon sequencing and droplet digital PCR, drinking water microbial community composition and DWPI density were examined. Microbial community composition analysis suggested significant compositional changes after the orthophosphate addition. Significant increases in total bacterial density were observed after orthophosphate addition, likely driven by a 2 log 10 increase in nontuberculous mycobacteria (NTM). Linear effect models confirmed the importance of phosphate addition with phosphorus concentration explaining 17% and 12% of the variance in NTM and L. pneumophila density, respectively. To elucidate the impact of phosphate on NTM aggregation, a comparison of planktonic and aggregate fractions of NTM cultures grown at varying phosphate concentrations was conducted. Aggregation assay results suggested that higher phosphate concentrations cause more disaggregation, and the interaction between phosphate and NTM is species specific. This work reveals new insight into the consequences of orthophosphate application on the DWDS microbiome and highlights the importance of proactively monitoring the DWDS for DWPIs.

Severe Prolonged Drought Favours Stress-Tolerant Microbes in Australian Drylands

Drylands comprise one-third of Earth’s terrestrial surface area and support over two billion people. Most drylands are projected to experience altered rainfall regimes, including changes in total amounts and fewer but larger rainfall events interspersed by longer periods without rain. This transition will have ecosystem-wide impacts but the long-term effects on microbial communities remain poorly quantified. We assessed belowground effects of altered rainfall regimes (+ 65% and -65% relative to ambient) at six sites in arid and semi-arid Australia over a period of three years (2016–2019) coinciding with a significant natural drought event (2017–2019). Microbial communities differed significantly among semi-arid and arid sites and across years associated with variation in abiotic factors, such as pH and carbon content, along with rainfall. Rainfall treatments induced shifts in microbial community composition only at a subset of the sites (Milparinka and Quilpie). However, differential abundance analyses revealed that several taxa, including Acidobacteria, TM7, Gemmatimonadates and Chytridiomycota, were more abundant in the wettest year (2016) and that their relative abundance decreased in drier years. By contrast, the relative abundance of oligotrophic taxa such as Actinobacteria, Alpha-proteobacteria, Planctomycetes, and Ascomycota and Basidiomycota, increased during the prolonged drought. Interestingly, fungi were shown to be more sensitive to the prolonged drought and to rainfall treatment than bacteria with Basidiomycota mostly dominant in the reduced rainfall treatment. Moreover, correlation network analyses showed more positive associations among stress-tolerant dominant taxa following the drought (i.e., 2019 compared with 2016). Our result indicates that such stress-tolerant taxa play an important role in how whole communities respond to changes in aridity. Such knowledge provides a better understanding of microbial responses to predicted increases in rainfall variability and the impact on the functioning of semi-arid and arid ecosystems.

Illegal Dumping of Oil and Gas Wastewaters Alters Semi-Arid Soil Microbial Communities

The Permian Basin, underlying New Mexico and Texas, is one of the most productive oil and gas (OG) provinces in the United States. Oil and gas production yields large volumes of wastewater with complex chemistries. The environmental health risks posed by these OG wastewaters are not well understood, particularly in the case of accidental or intentional releases. Starting in November 2017, 39 illegal dumps of OG wastewater were identified in southeastern New Mexico that released approximately 6.4x105 liters of fluid onto desert soils. To evaluate the impacts of these releases on soils, we analyzed changes in soil geochemistry and microbial community composition by comparing soils from within OG wastewater dump-affected zones to corresponding unaffected zones with no known releases. We observed significant (p&amp;lt;0.01) changes in soil geochemistry for all dump-affected samples compared to controls, reflecting the residual salts and hydrocarbons left behind by the OG-wastewater release (e.g., enriched in sodium (Na), chloride (Cl), and bromide (Br)). Illumina 16S iTag sequencing revealed significant (p&amp;lt;0.01) differences in microbial community structure between dump and control zones. Furthermore, soils from dump areas had significantly (p&amp;lt;0.01) lower alpha diversity and exhibited differences in phylogenetic composition. Dump-affected soil samples showed an increase in halophilic and halotolerant taxa, such as members of the Marinobacteraceae, Halomonadaceae, and Halobacteroidaceae, suggesting that the high salinity of the dumped OG wastewater exerted a selective pressure on microbial communities. Taxa related to known hydrocarbon-degrading organisms, e.g., Marinobacter, Salegentibacter, Chromohalobacter, and Alcanivorax, were also detected in the dump-affected soil-sample communities. The microbial communities in control soils were dominated by taxa ubiquitous in, and well adapted to, arid and nutrient-deprived soil environments including photosynthetic Cyanobacteria, hydrogen-oxidizing Actinobacteria and Acidobacteria, and nitrogen-fixing Alphaproteobacteria. This study demonstrated that OG-wastewater dumps can lead to shifts in microbial community composition and function towards salt- and hydrocarbon-tolerant taxa that are not typically found in desert soils, thus altering the impacted dryland soil ecosystem. Loss of key microbial taxa, such as those that increase arid soil fertility, or promote plant health, could result in cascading affects to myriad ecosystem services such as loss of flora. Further studies are needed to explore the potential for using halophilic and hydrocarbon-degrading taxa to bioremediate OG-wastewater affected lands.

Linking soil depth to aridity effects on soil microbial community composition, diversity and resource limitation

With ongoing climate change, aridity is increasing worldwide, affecting biodiversity and ecosystem function in drylands. However, how the depth-profile microbial community structure and metabolic limitations change along aridity gradients are still poorly explored. Here, 16S rRNA and ITS amplicon sequencing and ecoenzymatic stoichiometry analysis were used to investigate both bacterial and fungal diversities and resource limitations in 1 m depth profiles across a wide aridity gradient (0.51–0.78) in a semiarid region. Results showed a sharp decrease in microbial diversity with soil depth, accompanied by an increase in microbial phosphorus (P) vs. N (nitrogen) limitation and a decrease in microbial carbon (C) vs. nutrient limitation. Aridity led to a strong shift in microbial community composition, but aridity has a threshold effect on microbial resource limitation through impacts on soil pH and C/P or N/P. When the aridity threshold (1-precipitation/evapotranspiration) exceeds 0.65, relationship between aridity and microbial resource demand was decoupled; but at aridity threshold = 0.65, microbial relative C limitation and C-acquiring enzyme activity dropped. These results suggest that aridity might have a stronger influence on microbial community composition, than on diversity, shaped by inherent soil biotic factors (i.e., MBC:MBP or MBN:MBP). These findings suggest that soil microbial diversity or enzymatic stoichiometry may be not necessary to mirror changes in water availability in the drylands, while aridity would be well explained by microbial community composition.

Inhibition of nitrous oxide reduction in forest soil microcosms by different forms of methanobactin.

Copper plays a critical role in controlling greenhouse gas emissions as it is a key component of the particulate methane monooxygenase and nitrous oxide reductase. Some methanotrophs excrete methanobactin (MB) that has an extremely high copper affinity. As a result, MB may limit the ability of other microbes to gather copper, thereby decreasing their activity as well as impacting microbial community composition. Here, we show using forest soil microcosms that multiple forms of MB; MB from Methylosinus trichosporium OB3b (MB-OB3b) and MB from Methylocystis sp. strain SB2 (MB-SB2) increased nitrous oxide (N2 O) production as well caused significant shifts in microbial community composition. Such effects, however, were mediated by the amount of copper in the soils, with low-copper soil microcosms showing the strongest response to MB. Furthermore, MB-SB2 had a stronger effect, likely due to its higher affinity for copper. The presence of either form of MB also inhibited nitrite reduction and generally increased the presence of genes encoding for the iron-containing nitrite reductase (nirS) over the copper-dependent nitrite reductase (nirK). These data indicate the methanotrophic-mediated production of MB can significantly impact multiple steps of denitrification, as well as have broad effects on microbial community composition of forest soils.

Effects of rye inclusion in dog food on fecal microbiota and short-chain fatty acids

BackgroundRye intake has been associated with beneficial effects on health in human interventions, possibly due to dietary fiber in rye. In dogs, few studies have explored the effects on health of dietary fiber in general, and rye fiber in particular. The aim of this study was to investigate how inclusion of rye, compared with wheat, influenced fecal microbiota composition, short chain fatty acids (SCFA) and apparent total tract digestibility (ATTD) in dogs. Six male Beagle dogs (mean age 4.6 years, SEM 0.95 years; mean body weight 14.6 kg, SEM 0.32 kg) were fed three experimental diets, each for 21 days, including an adaptation period of six days and with 2–2.5 months between diet periods. The diets were similar regarding energy and protein, but had different carbohydrate sources (refined wheat (W), whole grain rye (R), or an equal mixture of both (RW)) comprising 50% of total weight on a dry matter (DM) basis. The diets were baked and titanium dioxide was added for ATTD determination. Fecal samples were collected before and in the end of each experimental period. Fecal microbiota was analyzed by sequencing 16S rRNA gene amplicons and fecal SCFA by high-performance liquid chromatography. Crude protein, crude fat, neutral detergent fiber, and gross energy (GE) in food and feces were analyzed and ATTD of each was determined. Univariate and multivariate statistical methods were applied in data evaluation.ResultsFaecal microbiota composition, differed depending on diet (P = 0.002), with samples collected after consumption of the R diet differing from baseline. This was primarily because of a shift in proportion of Prevotella, which increased significantly after consumption of the R diet (P < 0.001). No significant differences were found for SCFA, but there was a tendency (P < 0.06) for higher molar proportions of acetic acid following consumption of the R diet. The ATTD of crude protein, crude fat, neutral detergent fiber, and GE was lower after consumption of the R diet compared with the other diets (P < 0.05).ConclusionsConsumption of the R diet, but not RW or W diets, was associated with specific shifts in microbial community composition and function, but also with lower ATTD.

Taxonomical and functional responses of microbial communities from forest soils of differing tree species diversity to drying-rewetting cycles

The predicted increases in drought in many forest ecosystems may alter soil microbial community diversity and activity, which may further depend on tree species richness. Shifts in microbial community composition and activity could engender changes in ecosystem function, notably, in soil greenhouse gas emissions and C storage. Using soils from mono-specific and mixed three-species forest stands from across Europe, we performed a microcosm experiment to test how soil microbial taxonomic and catabolic diversity are affected by repeated drying-rewetting (DRW) cycles and tree species mixing. We used Illumina sequencing and MicroResp™ analyses to explore community-level changes between microbial functional groups. DRW decreased bacterial richness and carbon substrate use diversity and increased fungal Shannon diversity. Additionally, microbial communities exposed to DRW changed their consumption of 11 out of 15 substrates significantly, suggesting microbial functional shifts. The legacy effect of tree species mixing influenced the structure of the microbial communities (i.e. taxonomic differential abundance) although, community weighted mean (CWM) values of absorptive root traits appeared to affect more strongly microbial richness, relative abundance, and Shannon diversity. No significant tree species mixing:DRW interaction was found for most microbial variables, except for the use of certain substrates and potentially differential abundance. Our data from a laboratory experiment with soils from different forest ecosystems underline that drought may cause shifts in microbial taxonomic and catabolic diversity, while tree species influences primarily taxonomic diversity through root traits.

Reintroducing a keystone bioturbator can facilitate microbial bioremediation in urban polluted sediments

Anthropogenic environmental stressors have significantly reduced biodiversity and the capacity of remnant natural habitats to deliver ecosystem functions and services in urban areas. To mitigate these impacts and recover biodiversity and function, ecological restoration strategies are needed. While habitat restoration is proliferating in rural and peri-urban areas, strategies purposely designed to succeed under the environmental, social and political pressures of urban areas are lacking. Here, we propose that ecosystem health in marine urban areas can be improved by restoring biodiversity to the most dominant habitat, unvegetated sediments. We reintroduced a native ecosystem engineer, the sediment bioturbating worm Diopatra aciculata, and assessed their effects on microbial biodiversity and function. Results showed that worms can affect the diversity of microbes, but effects varied between locations. Worms caused shifts in microbial community composition and function at all locations. Specifically, the abundance of microbes capable of chlorophyll production (i.e. benthic microalgae) increased and the abundance of microbes capable of methane production decreased. Moreover, worms increased the abundances of microbes capable of denitrification in the site with lowest sediment oxygenation. Worms also affected microbes capable of degrading the polycyclic aromatic hydrocarbon toluene, although the direction of that effect was site-specific. This study provides evidence that a simple intervention such as the reintroduction of a single species can enhance sediment functions important for the amelioration of contamination and eutrophication, although further studies are needed to understand the variation in outcomes between sites. Nevertheless, restoration strategies targeting unvegetated sediments provide an opportunity to combat anthropogenic stressors in urban ecosystems and may be used for precondition before more traditional forms of habitat restoration such as seagrass, mangrove and shellfish restoration.

Community Level Physiological Profiling of Microbial Communities Influencing Mine Spoil Genesis in Chronosequence Coal Mine Overburden Spoil

Ecological restoration through mine spoil genesis should be dogmatic and the strategies involved a holistic approach, which emphasizes the role of microbial community composition that varies in accordance with the physiological and nutritional status of mine spoil profiles. This is because the patterns observed aboveground is being driven by the belowground diversity and processes. Thus, the relationship between microbial community structure and mine spoil genesis in chronosequence coal mine spoil has attracted considerable research attention. The occurrence of higher microbial diversity and difficulties in culturing microbes necessitate the use of a culture-independent approach through community-level physiological profiling based on the patterns of carbon source utilization using BIOLOG Ecoplate and thereby the functional diversity of microbial communities in different age series coal mine spoil was determined. The average well-color development exhibited an increasing trend with a minimum in OB0 (0.0640) and a maximum in OB15 (0.5060) over time. The patterns of substrate utilization (carbohydrates, carboxylic and ketonic acids, amino acids, polymers, amines, and amides) reflect the shift in microbial community composition in different age series coal mine spoil over time. Gradual increase in species richness and Shannon diversity index with the increase in age of mine spoil substantiated relatively higher microbial diversity reflecting the sign of mine spoil genesis. Principal component analysis and redundancy analysis based on the differential patterns of substrate utilization discriminate different age series coal mine spoil into independent clusters, which evaluated the broad-scale patterns of microbial community dynamics influencing the pace and progress of mine spoil genesis.

Suppression of Phytophthora on Chamaecyparis in Sustainable Horticultural Substrates Depends on Fertilization and Is Linked to the Rhizobiome

Nature management residues (i.e., biomass generated from the management of nature reserves) are promising peat alternatives for horticultural substrates and may have a positive effect on disease suppression because of their microbiological characteristics. Moreover, addition of fertilizer may also affect the rhizosphere microbiome and, accordingly, disease suppression. In this study, we determined the effect of two management residues in horticultural substrates (i.e., chopped heath and acidified soft rush) and two fertilization regimes (i.e., pure nitrogen fertilizer and compound fertilizer) on the suppression of Phytophthora spp. on Chamaecyparis lawsoniana. The bacterial and fungal rhizosphere community was characterized using 16S ribosomal RNA and internal transcribed spacer 2 gene metabarcoding. Soft rush with a compound fertilizer (R2) and chopped heath with a pure nitrogen fertilizer (H1) showed a disease-suppressive effect and showed the largest shifts in microbial community composition compared with peat-based substrates. The disease-suppressive treatments showed differences in their microbial communities. Different genera associated with described biocontrol agents for Phytophthora spp. were found in higher amounts in those treatments. Aspergillus and Trichoderma spp. were highly abundant in H1, while Actinomadura and Bacillus spp. had a high abundance in R2. In addition, the relative abundances of 24 bacterial and 9 fungal genera were negatively correlated with disease severity. Several of those genera, including Bacillus, Chaetomium, and Actinomadura, were significantly more abundant in one of the disease-suppressive treatments. This study shows that disease suppressiveness in sustainable horticultural substrates is dependent on fertilization and can be linked to changes in the microbial rhizosphere communities.

Composition and factors influencing community structure of lactic acid bacterial in dairy products from Nyingchi Prefecture of Tibet

This study investigated the community composition of lactic acid bacteria (LAB) from yaks' milk (YM) Tibetan yellow cattle milk (TM) and their fermented products from different counties in the Nyingchi Prefecture, Tibet using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing. Sequencing revealed 26 genera and 94 species from 71 dairy samples; amongst these Lactobacillus delbrueckii (36.17%), Streptococcus thermophilus (19.46%) and Lactococcus lactis (18.33%) were the predominant species. This study also identified the main factors influencing LAB community composition by comparing amongst samples from different locations, from different milk types, and from different altitudes. The LAB communities in YM and TM were more diverse than in fermented yaks' milk (FYM) and fermented Tibetan yellow cattle milk (FTM) samples. Similarly, whether milk was fermented or not accounted for differences in LAB species composition while altitude of the dairy products had very little effect. Milk source and production process were the most likely causes of drastic shifts in microbial community composition. In addition, fermented dairy products were enriched in genes responsible for secondary metabolic pathways that were potentially beneficial for health. Comprehensive descriptions of the microbiota in different dairy products from the Nyingchi Prefecture, Tibet might help elucidate evolutionary and functional relationships amongst bacterial communities in these products.

Exploring the Impacts of Full-Scale Distribution System Orthophosphate Corrosion Control Implementation on the Microbial Ecology of Hydrologically Connected Urban Streams.

Many cities across the nation are plagued by lead contamination in drinking water. As such, many drinking water utilities have undertaken lead service line (LSL) replacement to prevent further lead contamination. However, given the urgency of lead mitigation, and the socioeconomic challenges associated with LSL replacement, cities have used phosphate-based corrosion inhibitors (i.e., orthophosphate) alongside LSL replacement. While necessary to ensure public health protection from lead contamination, the addition of orthophosphate into an aging and leaking drinking water system may increase the concentration of phosphate leaching into urban streams characterized by century-old failing water infrastructure. Such increases in phosphate availability may cascade into nutrient and microbial community composition shifts. The purpose of this study was to determine how this occurs and to understand whether full-scale distribution system orthophosphate addition impacts the microbial ecology of urban streams. Through monthly collection of water samples from five urban streams before and after orthophosphate addition, significant changes in microbial community composition (16S rRNA amplicon sequencing) and in the relative abundance of typical freshwater taxa were observed. In addition, key microbial phosphorus and nitrogen metabolism genes (e.g., two component regulatory systems) were predicted to change via BugBase. No significant differences in the absolute abundances of total bacteria, Cyanobacteria, and "Candidatus Accumulibacter" were observed. Overall, the findings from this study provide further evidence that urban streams are compromised by unintentional hydrologic connections with drinking water infrastructure. Moreover, our results suggest that infiltration of phosphate-based corrosion inhibitors can impact urban streams and have important, as-yet-overlooked impacts on urban stream microbial communities. IMPORTANCE Elevated lead levels in drinking water supplies are a public health risk. As such, it is imperative for cities to urgently address lead contamination from aging drinking water supplies by way of lead service line replacements and corrosion control methods. However, when applying corrosion control methods, it is also important to consider the chemical and microbiological effects that can occur in natural settings, given that our water infrastructure is aging and more prone to leaks and breaks. Here, we examine the impacts on the microbial ecology of five urban stream systems before and after full-scale distribution system orthophosphate addition. Overall, the results suggest that infiltration of corrosion inhibitors may impact microbial communities; however, future work should be done to ascertain the true impact to protect both public and environmental health.

High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS

Microbial communities are inter-connected systems of incredible complexity and dynamism that play crucial roles in health, energy, and the environment. To better understand microbial communities and how they respond to change, it is important to know which microbes are present and their relative abundances at the greatest taxonomic resolution possible. Here, we describe a novel protocol (RoC-ITS) that uses the single-molecule Nanopore sequencing platform to assay the composition of microbial communities at the subspecies designation. Using rolling-circle amplification, this methodology produces long-read sequences from a circular construct containing the complete 16S ribosomal gene and the neighboring internally transcribed spacer (ITS). These long reads can be used to generate a high-fidelity circular consensus sequence. Generally, the ribosomal 16S gene provides phylogenetic information down to the species-level, while the much less conserved ITS region contains strain-level information. When linked together, this combination of markers allows for the identification of individual ribosomal units within a specific organism and the assessment of their relative stoichiometry, as well as the ability to monitor subtle shifts in microbial community composition with a single generic assay. We applied RoC-ITS to an artificial microbial community that was also sequenced using the Illumina platform, to assess its accuracy in quantifying the relative abundance and identity of each species.