Microbial Community Shifts Research Articles

Plant species, nitrogen status and endophytes are drivers of soil microbial communities in grasslands

Context There is concern that the introduction of ‘novel’ plant germplasm/traits could outpace our capacity to measure and so assess their impacts on soil microbial communities and function. Aim This study aimed to investigate the effects of plant species/functional traits, nitrogen (N) fertilisation and endophyte infection on grassland soil microbial communities within a short time span of 2 years. Methods Two field experiments with monoculture plots were conducted in a common soil. Experiment 1 compared grasses and legumes, using two cultivars of perennial ryegrass (Lolium perenne) that varied in fructan content, along with the legumes white clover (Trifolium repens) and bird’s-foot trefoil (Lotus pedunculatus) that varied in tannin content. Grass treatments received high and low N application levels. Experiment 2 compared the presence/absence of Epichloë strains in ryegrass, tall fescue (Schedonorus phoenix) and meadow fescue (Schedonorus pratensis). Soil microbial communities were analysed by using high-throughput sequencing of DNA isolated from bulk soil cores. Key results Higher abundance of ligninolytic fungi was found in grass soils and pectinolytic fungi in legume soils. Levels of N fertilisation and fructan in ryegrass had only minor effects on soil fungal communities. By contrast, N fertilisation or fixation had a strong effect on bacterial communities, with higher abundance of nitrifiers and denitrifiers in high-N grass soils and in legume soils than in low-N grass soils. Epichloë affected soil microbiota by reducing the abundance of certain fungal phytopathogens, increasing mycorrhizal fungi and reducing N-fixing bacteria. Conclusions Chemical composition of plant cell walls, which differs between grasses and legumes, and presence of Epichloë in grasses were the main drivers of shifts in soil microbial communities. Implications Impacts of farming practices such as mono- or poly-culture, N fertilisation and presence of Epichloë in grasses on soil microbial communities should be considered in pasture management.

Soil microbial community shifts explain habitat heterogeneity in two Haloxylon species from a nutrient perspective.

Haloxylon ammodendron and Haloxylon persicum (as sister taxa) are dominant shrubs in the Gurbantunggut Desert. The former grows in inter-dune lowlands while the latter in sand dunes. However, little information is available regarding the possible role of soil microorganisms in the habitat heterogeneity in the two Haloxylon species from a nutrient perspective. Rhizosphere is the interface of plant-microbe-soil interactions and fertile islands usually occur around the roots of desert shrubs. Given this, we applied quantitative real-time PCR combined with MiSeq amplicon sequencing to compare their rhizosphere effects on microbial abundance and community structures at three soil depths (0-20, 20-40, and 40-60 cm). The rhizosphere effects on microbial activity (respiration) and soil properties had also been estimated. The rhizospheres of both shrubs exerted significant positive effects on microbial activity and abundance (e.g., eukarya, bacteria, and nitrogen-fixing microbes). The rhizosphere effect of H.ammodendron on microbial activity and abundance of bacteria and nitrogen-fixing microbes was greater than that of H.persicum. However, the fertile island effect of H.ammodendron was weaker than that of H.persicum. Moreover, there existed distinct differences in microbial community structure between the two rhizosphere soils. Soil available nitrogen, especially nitrate nitrogen, was shown to be a driver of microbial community differentiation among rhizosphere and non-rhizosphere soils in the desert. In general, the rhizosphere of H.ammodendron recruited more copiotrophs (e.g., Firmicutes, Bacteroidetes, and Proteobacteria), nitrogen-fixing microbes and ammonia-oxidizing bacteria, and with stronger microbial activities. This helps it maintain a competitive advantage in relatively nutrient-rich lowlands. Haloxylon persicum relied more on fungi, actinomycetes, archaea (including ammonia-oxidizing archaea), and eukarya, with higher nutrient use efficiency, which help it adapt to the harsher dune crests. This study provides insights into the microbial mechanisms of habitat heterogeneity in two Haloxylon species in the poor desert soil.

Pollutants removal, microbial community shift and oleic acid production in symbiotic microalgae–bacteria system

The functional interaction between microorganisms is key in symbiotic microalga–bacteria systems; however, evaluations of fungi and pathogenic microorganisms are not clear. In this study, the roles of three groups (i.e., microalgae–activated sludge (MAS), Microalgae, and activated sludge) in pollutant removal and biomass recovery were comparatively studied. The data implied that microalgal assimilation and bacterial heterotrophic degradation were the major approaches for degradation of nutrients and organic matter, respectively. According to 16S rRNA and internal transcribed spacer sequencing, the relative abundance of Rhodotorula increased remarkably, favoring nutrient exchange between the microalgae and bacteria. The abundances of two types of pathogenic genes (human pathogens and animal parasites) were reduced in the MAS system. The oleic acid content in the MAS system (51.2 mg/g) was 1.7 times higher than that in the Microalgae system. The results can provide a basis for practical application and resource utilization of symbiotic microalgae–bacteria systems.

Biogeographic distributions of microbial communities associated with anaerobic methane oxidation in the surface sediments of deep-sea cold seeps in the South China Sea.

Cold seeps are oasis for the microbes in the deep-sea ecosystems, and various cold seeps are located along the northern slope of the South China Sea (SCS). However, by far most microbial ecological studies were limited to specific cold seep in the SCS, and lack of comparison between different regions. Here, the surface sediments (0-4 cm) from the Site F/Haima cold seeps and the Xisha trough in the SCS were used to elucidate the biogeography of microbial communities, with particular interest in the typical functional groups involved in the anaerobic oxidation of methane (AOM) process. Distinct microbial clusters corresponding to the three sampling regions were formed, and significantly higher gene abundance of functional groups were present in the cold seeps than the trough. This biogeographical distribution could be explained by the geochemical characteristics of sediments, such as total nitrogen (TN), total phosphorus (TP), nitrate (NO3 -), total sulfur (TS) and carbon to nitrogen ratios (C/N). Phylogenetic analysis demonstrated that mcrA and pmoA genotypes were closely affiliated with those from wetland and mangroves, where denitrifying anaerobic methane oxidation (DAMO) process frequently occurred; and highly diversified dsrB genotypes were revealed as well. In addition, significantly higher relative abundance of NC10 group was found in the Xisha trough, suggesting that nitrite-dependent DAMO (N-DAMO) process was more important in the hydrate-bearing trough, although its potential ecological contribution to AOM deserves further investigation. Our study also further demonstrated the necessity of combining functional genes and 16S rRNA gene to obtain a comprehensive picture of the population shifts of natural microbial communities among different oceanic regions.

Granular activated carbon stimulated microbial extracellular secretions in anaerobic digesters: An egalitarian act and beyond

Granular activated carbon (GAC) has been widely studied for its roles in improving anaerobic digestion (AD) through its conductive properties in stimulating direct interspecies electron transfer or its surface functional groups in altering redox conditions in AD. In the present study, the impacts of GAC on the biosynthesis of extracellular microbial secretions (e.g., amino acids and vitamins), and the roles of these secretions in AD were investigated. Four continuous laboratory reactors were operated under ambient temperature (20 ± 0.5 °C) conditions, including two up-flow anaerobic sludge blanket (UASB) bioreactors with GAC addition to one of the UASBs; and two anaerobic sequencing batch reactors (ASBRs) each fed with the centrifuged supernatants (to remove suspended biomass and GAC debris) of UASB effluents supplemented with additional carbon source (glucose). Our finding shows that GAC addition stimulated extracellular microbial secretions in UASB, and these secretions, which can work as essential nutrients, enhanced COD removal (from 48 ± 3 % to 60 ± 1 %) and methane production (31 ± 3 % to 47 ± 5 %) in its downstream ASBR. Interestingly, microbial kinetics test showed that extracellular microbial secretions from the GAC-amended UASB improved methane production rate from 72.5 ± 1.5 to 105.6 ± 1.2 mg CH4-COD/g VSS/d without dramatic microbial community shift. We conclude that the impact of GAC on AD does not only rely on the direct contact of microorganisms and GAC materials, and the GAC-stimulated microbial extracellular secretions represent an important mechanism in conductive material amended AD.

Impact of ileal indigestible protein on fecal nitrogen excretion and fecal microbiota may be greater compared with total protein concentration of diets in growing pigs.

In the current study, we hypothesized that an increase in dietary ileal indigestible protein concentration induces an increase in hindgut nitrogen utilization and nitrogen excretion and a shift in fecal microbiota in growing pigs, when compared to pigs given a high total protein diet. Three diets were prepared: 1) standard protein diet based on corn and soybean meal, 2) high-indigestible protein diet in which autoclaved, low-digestible soybean meal replaced soybean meal in the first diet, and 3) high protein diet where the inclusion rate of soybean meal was greater than that of the other diets. The 3 diets were fed to 18 barrows that were fitted with T-cannula at the ileo-cecal junction (initial body weight = 63.4 ± 8.0 kg) in a randomized complete block design with body weight as a blocking factor. Pigs were individually housed in pens and the experiment lasted for 23 d. On days 7 and 21, fecal samples were collected by rectal massage for microbiota analysis. Grab samples of feces were collected on days 20 and 21, and ileal digesta were collected on days 22 and 23 for the determination of energy and nitrogen utilization. Lower apparent ileal digestibility of nitrogen in the high-indigestible protein diet containing autoclaved soybean meal resulted in greater ileal indigestible nitrogen concentration (P < 0.05). Apparent total tract digestibility of nitrogen was lower (P < 0.05), and correspondingly nitrogen concentration and daily fecal nitrogen output were greater (P < 0.05) in the high-indigestible protein diet compared with the other diets. Apparent post-ileal digestibility and hindgut disappearance of nitrogen and gross energy were the greatest (P < 0.05) in the high protein diet, whereas a statistical difference was not observed in those variables between the standard protein diet and the high-indigestible protein diet. Beta diversity metrics of feces in the high-indigestible protein diet on day 21 were different (q < 0.05) from those in the other two diets, which indicates a shift in microbial communities. According to the results of the DESeq2, the direction of microbiota shift induced by the high-indigestible protein diet may have reduced fiber utilization in the hindgut. In conclusion, an increase in dietary ileal indigestible protein concentration increased fecal nitrogen excretion and shifted fecal microbial communities but did not increase nitrogen utilization in the hindgut.

Power Generation and Microbial Community Shift According to Applied Anodic Potential in Electroactive Biofilm Reactors Treating Synthetic and Domestic Wastewater

This study investigated the effect of initially set anodic potentials (−0.3, −0.2, −0.1 and +0.1 V) on voltage production and microbial community in electroactive biofilm reactors (EBRs) treating synthetic and domestic wastewater (WW). In phase 1, EBRs were acclimated with different anodic potentials for synthetic and domestic WW. EBR (SE4) poised with +0.1 V showed the highest maximum power density (420 mW/m2) for synthetic WW, while EBR (DE3) poised with −0.1 V showed the highest maximum power density (235 mW/m2) for domestic WW. In phase 2, the EBRs were operated with a fixed external resistance (100 Ω for synthetic WW and 500 Ω for domestic WW) after the applied potentials were stopped. The EBRs showed slightly different voltage productions depending on the WW type and the initial anodic potential, but both EBRs applied with +0.1 V for synthetic (SE4) and domestic (DE4) WW showed the highest voltage production. Principal component analysis results based on denaturing gel gradient electrophoresis band profiles showed that the microbial community was completely different depending on the WW type. Nevertheless, it was found that the microbial community of EBRs applied with a negative potential (−0.3, −0.2, and −0.1 V) seemed to shift to those of EBRs applied with a positive potential (+0.1 V) regardless of WW type. Therefore, positive anodic potential is an important operating factor in electroactive biofilm development and voltage generation for rapid start-up.

Effect of Toxic Phthalate-Based Plasticizer on the Biodegradability of Polyhydroxyalkanoate

While new biodegradable materials are being rapidly introduced to address plastic pollution, their end-of-life impacts remain unclear. Biodegradable plastics typically comprise a biopolymer matrix with functional additives and/or solid fillers, which may be toxic. Here, using an established method for continuous biodegradation monitoring, we investigated the impact of a commonly used plasticizer, dibutyl phthalate (DBP), on the biodegradation of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) in soil. The presence of DBP delayed the initial stage of PHBV biodegradation but then accelerated subsequent rates of biodegradation. Furthermore, it led to significant increases in total bacterial and fungal biomass and altered the composition of microbial communities with significant increases in the relative abundances of Thauera (gammaproteobacterial) and Mucor circinelloides (fungal) populations. It is proposed, with evidence from biodegradation behavior and microbial analysis, that the presence of DBP likely stimulated a microbial community shift, introduced higher proportions of more readily degradable amorphous regions from the plasticizing effect, and facilitated access to the bulk polymer matrix for microorganisms or at least their associated enzymes. These effects in combination overcame the initial inhibition effect of the DBP and resulted in a net increase in the rate of biodegradation of PHBV.

Microbial biomarkers as indication of dynamic and heterogeneous urban water environments.

Water samples for the 16S rRNA gene and water quality analyses were collected from around 155km of river segments surrounding the urban areas in Xi'an, China. Multiple statistical analyses showed that the dynamic shifts of microbial communities in the Chan, Ba, and Feng Rivers from the spring to the summer seasons were apparent but little in the Zao River. The heterogeneity of microbial distributions was more due to the influence of hydrologic conditions and various sources of inflows in the rivers. The LEfSe analysis showed that the Chan and Zao Rivers, both more impacted by the sewage effluents, were more differentially abundant with bacteria related to polluted water, but the Ba and Feng Rivers, both on the outer side of the city, were more abundant with microbial communities in soil and freshwater environments in the summer. Multiple statistical analyses indicated that environmental variables had significant impacts on microbial communities. The geographical information system-based spatial analysis showed heterogeneity of microbial community distributions along the rivers. This study showed that the high-throughput sequencing analysis could identify some pathogenic bacteria that would significantly threaten public health and eco-environments in urban rivers.

Resilience of ecosystem service delivery in grasslands in response to single and compound extreme weather events

Extreme weather events are increasing in frequency and magnitude with profound effects on ecosystem functioning. Further, there is now a greater likelihood that multiple extreme events are occurring within a single year. Here we investigated the effect of a single drought, flood or compound (flood + drought) extreme event on temperate grassland ecosystem processes in a field experiment. To assess system resistance and resilience, we studied changes in a wide range of above- and below-ground indicators (plant diversity and productivity, greenhouse gas emissions, soil chemical, physical and biological metrics) during the 8 week stress events and then for 2 years post-stress. We hypothesized that agricultural grasslands would have different degrees of resistance and resilience to flood and drought stress. We also investigated two alternative hypotheses that the combined flood + drought treatment would either, (A) promote ecosystem resilience through more rapid recovery of soil moisture conditions or (B) exacerbate the impact of the single flood or drought event. Our results showed that flooding had a much greater effect than drought on ecosystem processes and that the grassland was more resistant and resilient to drought than to flood. The immediate impact of flooding on all indicators was negative, especially for those related to production, and climate and water regulation. Flooding stress caused pronounced and persistent shifts in soil microbial and plant communities with large implications for nutrient cycling and long-term ecosystem function. The compound flood + drought treatment failed to show a more severe impact than the single extreme events. Rather, there was an indication of quicker recovery of soil and microbial parameters suggesting greater resilience in line with hypothesis (A). This study clearly reveals that contrasting extreme weather events differentially affect grassland ecosystem function but that concurrent events of a contrasting nature may promote ecosystem resilience to future stress.

Quantifying (non)parallelism of gut microbial community change using multivariate vector analysis.

Parallel evolution of phenotypic traits is regarded as strong evidence for natural selection and has been studied extensively in a variety of taxa. However, we have limited knowledge of whether parallel evolution of host organisms is accompanied by parallel changes of their associated microbial communities (i.e., microbiotas), which are crucial for their hosts' ecology and evolution. Determining the extent of microbiota parallelism in nature can improve our ability to identify the factors that are associated with (putatively adaptive) shifts in microbial communities. While it has been emphasized that (non)parallel evolution is better considered as a quantitative continuum rather than a binary phenomenon, quantitative approaches have rarely been used to study microbiota parallelism. We advocate using multivariate vector analysis (i.e., phenotypic change vector analysis) to quantify direction and magnitude of microbiota changes and discuss the applicability of this approach for studying parallelism, and we compiled an R package for multivariate vector analysis of microbial communities ('multivarvector'). We exemplify its use by reanalyzing gut microbiota data from multiple fish species that exhibit parallel shifts in trophic ecology. We found that multivariate vector analysis results were largely consistent with other statistical methods, parallelism estimates were not affected by the taxonomic level at which the microbiota is studied, and parallelism might be stronger for gut microbiota function compared to taxonomic composition. This approach provides an analytical framework for quantitative comparisons across host lineages, thereby providing the potential to advance our capacity to predict microbiota changes. Hence, we emphasize that the development and application of quantitative measures, such as multivariate vector analysis, should be further explored in microbiota research in order to better understand the role of microbiota dynamics during their hosts' adaptive evolution, particularly in settings of parallel evolution.

The effect of biochar on mycorrhizal fungi mediated nutrient uptake by coconut (Cocos nucifera L.) seedlings grown on a Sandy Regosol

Biochar amendment of soil may ameliorate inherently infertile soils, such as in the typical coconut (Cocos nucifera L.) growth areas along tropical coasts, where, moreover, temporary moisture stress commonly occurs. We conducted a pot experiment to evaluate the effects of biochar soil amendment (1% w/w) produced from Gliricidia sepium stems (BC-Gly) and rice husks (BC-RiH) on the growth of coconut seedlings and on N and P uptake mediated by mycorrhizae under wet or dry conditions in a Sandy Regosol. The pots were divided into root and hyphal zones by a nylon mesh, where 15N labelled N and P nutrients were only provided in the hyphal zone. Under wet conditions, biochar application did not affect plant growth, while under dry conditions, the BC-Gly increased root and plant growth similar to that under wet conditions. BC-Gly increased the acidic pH of the soil to a neutral level, and the microbial community shifted towards a higher fungal abundance. The P accumulated (Pacc) in roots was higher with BC-Gly and BC-RiH under dry and wet conditions, respectively. Pacc weakly correlated with the abundance of arbuscular mycorrhizal fungi (AMF) in the hyphal zone. With BC-Gly roots showed lower N derived from fertilizer. We conclude that biochar application has no impact on crop growth under wet conditions, while under dry conditions, BC-Gly stimulates crop growth and P uptake, probably through liming induced P availability but also possibly by some enhancement of AMF growth. The shift in the fungal-oriented microbial community and reduced plant fertilizer N uptake suggested that BC-Gly acted as an additional N source.Graphical

Eco-enzymatic stoichiometry and microbial non-homeostatic regulation depend on relative resource availability during litter decomposition

The relationships between soil eco-enzymatic stoichiometry and substrate stoichiometry could be used to explain nutrient cycling processes regulated by microbial biomass stoichiometry. But what are the relationships between the stoichiometry of resources, microorganisms, and enzymes? We do not have a clear understanding yet, particularly in the different stages of litter decomposition. By analyzing the response of extracellular enzymatic stoichiometry to the imbalance between microbial and substrate stoichiometry, we explore the microbial-mediated litter transformation and microbial adaptation mechanisms in the transformation interface soil (TIS) layer. The results showed that soil microbial metabolism was limited by C and P during decomposition, peaking in the transition (middle) stage and then gradually decreasing. According to the judgment of microbial homeostasis (effect of substrate stoichiometry on microbial biomass stoichiometry), the microbial communities shift from homeostatic in the early stage to non-homeostatic in the middle stage and then return to homeostasis in the later stage. During the litter decomposition, the non-homeostatic period corresponded to the transition stage. That means severe microbial metabolic limitation is a potential determinant of microbial homeostasis. Soil microorganisms adapt and alleviate microbial metabolic limitations by adjusting extracellular enzyme activity and microbial non-homeostatic behavior when the available resources fail to satisfy microbial requirements.

Foliar Pathogen Infection Manipulates Soil Health through Root Exudate-Modified Rhizosphere Microbiome.

Negative plant-soil feedback (NPSF) due to the buildup of soilborne pathogens in soil is a major obstacle in sustainable agricultural systems. Beneficial rhizosphere microfloras are recruited by plants, and mediating this has become a strategic priority to manipulate plant health. Here, we found that foliar infection of Panax notoginseng by Alternaria panax changed plant-soil feedback from negative to positive. Foliar infection modified the rhizosphere soil microbial community and reversed the direction of the buildup of the soilborne pathogen Ilyonectria destructans and beneficial microbes, including Trichoderma, Bacillus, and Streptomyces, in rhizosphere soil. These beneficial microbes not only showed antagonistic ability against the pathogen I. destructans but also enhanced the resistance of plants to A. panax. Foliar infection enhanced the exudation of short- and long-chain organic acids, sugars, and amino acids from roots. In vitro and in vivo experiments validated that short- and long-chain organic acids and sugars play dual roles in simultaneously suppressing pathogens but enriching beneficial microbes. In summary, foliar infection could change root secretion to drive shifts in the rhizosphere microbial community to enhance soil health, providing a new strategy to alleviate belowground disease in plants through aboveground inducement. IMPORTANCE Belowground soilborne disease is the main factor limiting sustainable agricultural production and is difficult to manage due to the complexity of the soil environment. Here, we found that aboveground parts of plants infected by foliar pathogens could enhance the secretion of organic acids, sugars, and amino acids in root exudates to suppress soilborne pathogens and enrich beneficial microbes, eventually changing the plant and soil feedback from negative to positive and alleviating belowground soilborne disease. This is an exciting strategy by which to achieve belowground soilborne disease management by manipulating the aboveground state through aboveground stimulation.

Long-term differences in fertilisation type change the bacteria:archaea:fungi ratios and reveal a heterogeneous response of the soil microbial ionome in a Haplic Luvisol

Organic farm management through farmyard manure application is associated with soil organic carbon sequestration facilitated by more balanced nutrient stoichiometry of macro- and micronutrients. Quantitative information on micronutrients within the soil microbial biomass is lacking. Using soils from a 40-year old long-term field trial (DOK), we investigated if fertilisation differences (farmyard manure equivalent to 0.7 or 1.4 livestock units per hectare and mineral fertilisation) and farm management (biodynamic, organic, conventional) changed the soil microbial ionome and stoichiometry and if this is related to microbial community shifts. Soil (15% sand, 70% silt and 15% clay) from the top 20 cm was analysed for microbial biomass carbon, nitrogen and phosphorus. Further elements were assessed via an adapted chloroform-fumigation extraction procedure. Abundances of bacteria, archaea, and fungi were determined (qPCR). Farmyard manure increased microbial biomass by approximately two-fold and the contribution of bacteria and archaea by up to approximately five-fold. Microbial biomass phosphorus and magnesium increased with mineral fertilisation (from 7 to 14 μg g−1 soil) and farmyard manure (from 0.5 to 2.7 μg g−1 soil), respectively. The microbial biomass carbon to potassium ratio remained similar, at around 47:1, revealing stoichiometric control. Microbial biomass manganese was reduced from 3.5 to 2.2 μg g−1 soil with lower availability due to raised pH in biodynamic management. The microbial stoichiometry and ionome were mainly affected by nutrient input and soil chemical properties; direct links between microbial (micronutrient-) stoichiometry and microbial community changes cannot be established with certainty due to potential confounding effects of pH changes.

Distinct roles of bacteria and fungi in mediating soil extracellular enzymes under long-term nitrogen deposition in temperate plantations

Soil microbes decompose soil organic matter by producing various extracellular enzymes, and also regulate soil carbon (C) and nutrient cycles. However, how shifts in soil microbial community under long-term nitrogen (N) deposition govern soil extracellular enzyme activities (EEAs) is not known. Here, we conducted a decade-long N fertilization experiment consisting of control, low-N (2 g N m−2 year−1), medium-N (5 g N m−2 year−1), and high-N (10 g N m−2 year−1) treatments in a N-limited temperate plantation in northern China. The diversity and community composition of fungi and bacteria were determined with bacterial 16S rRNA genes and fungal internal transcribed spacer genes sequencing. Soil EEAs involved in C, N, and phosphorus (P) cycles were also measured. The results showed that high-N addition increased fungal diversity and altered microbial community composition. In particular, rare fungal diversity and rare bacterial community composition were more sensitive to N addition. N addition improved β-1,4-glucosidase (BG) and acid phosphatase (AP) activities by altering bacterial community composition, and inhibited leucine aminopeptidase (LAP) and polyphenolic oxidase (PPO) activities by affecting fungal functional groups. Specifically, shifts in bacterial community composition caused by N addition were reflected in the significant increase in the dominant class Thermoleophilia, which could be an indicator of secreted hydrolase involved in C and P cycles. Symbiotrophic fungi were more closely associated with LAP for acquiring N and PPO. Our data provide a novel view of the link between major extracellular enzymes and specific microbial taxa under the background of N deposition.

Reshuffling of the Coral Microbiome during Dormancy.

Quiescence, or dormancy, is a response to stressful conditions in which an organism slows or halts physiological functioning. Although most species that undergo dormancy maintain complex microbiomes, there is little known about how dormancy influences and is influenced by the host's microbiome, including in the temperate coral Astrangia poculata. Northern populations of A. poculata undergo winter quiescence. Here, we characterized wild A. poculata microbiomes in a high-resolution sampling time series before, during, and after quiescence using 16S rRNA gene sequencing on active (RNA) and present (DNA) microbiomes. We observed a restructuring of the coral microbiome during quiescence that persisted after reemergence. Upon entering quiescence, corals shed copiotrophic microbes, including putative pathogens, suggesting a removal of these taxa as corals cease normal functioning. During and after quiescence, bacteria and archaea associated with nitrification were enriched, suggesting that the quiescent microbiome may replace essential functions through supplying nitrate to corals and/or microbes. Overall, this study demonstrates that key microbial groups related to quiescence in A. poculata may play a role in the onset or emergence from dormancy and long-term regulation of the microbiome composition. The predictability of dormancy in A. poculata provides an ideal natural manipulation system to further identify factors that regulate host-microbial associations. IMPORTANCE Using a high-resolution sampling time series, this study is the first to demonstrate a persistent microbial community shift with quiescence (dormancy) in a marine organism, the temperate coral Astrangia poculata. Furthermore, during this period of community turnover, there is a shedding of putative pathogens and copiotrophs and an enhancement of the ammonia-oxidizing bacteria (Nitrosococcales) and archaea ("Candidatus Nitrosopumilus"). Our results suggest that quiescence represents an important period during which the coral microbiome can reset, shedding opportunistic microbes and enriching for the reestablishment of beneficial associates, including those that may contribute nitrate while the coral animal is not actively feeding. We suggest that this work provides foundational understanding of the interplay of microbes and the host's dormancy response in marine organisms.

Application of Coagulation and Foam Concentration Method to Quantify Waterborne Pathogens in River Water Samples

One of the major challenges in detecting waterborne pathogens is the low concentration of the target bacteria in water. In this study, we applied the coagulation and foam concentration method to obtain DNA from water samples collected from upstream, near an estuary. The DNA samples were analyzed using 16S rRNA gene sequencing to clarify the microbial community shifts and to identify potentially pathogenic bacteria. Bacterial communities changed as the river flowed downstream, most likely influenced by land use and human activities such as the discharge of wastewater-treatment plant effluent. Based on the 16S rRNA gene amplicon sequencing, potentially pathogenic bacteria were detected with greater than 0.1% of their relative abundances. Among these, Yersinia ruckeri and Pseudomonas alcaligenes were widely detected in the river water. In addition, digital PCR (dPCR) was used to quantify major waterborne pathogens. Shiga toxin-producing Escherichia coli (STEC), Shigella spp., and Campylobacter jejuni were all below the limit of detection. In contrast, general E. coli, which has the beta-D-glucuronidase gene (uidA) were detected by dPCR (copies/100 mL) at similar levels to those measured using the culture-based method (as colony forming units/100 mL). These results suggest that the coagulation and foam concentration method is useful for concentrating microbes and obtaining DNA from river water samples for environmental monitoring.

Earthworm stocking density regulates microbial community structure and fatty acid profiles during vermicomposting of lignocellulosic waste: Unraveling the microbe-metal and mineralization-humification interactions

Earthworm-induced microbial enrichment is the key to success in vermitechnology, yet the influence of initial earthworm stocking density on microbial community profiles in vermibeds is unknown. Therefore, vermicomposting of lignocellulosic feedstock was performed with different stocking densities of two earthworms (Eisenia fetida and Eudrilus eugeniae) compared with composting. Eventually, earthworm growth, microbial (activity and community profiles), and physicochemical dynamics were assessed. The earthworm population significantly increased under low stocking, while denser stocking (15/kg) was stressful. The XRD-based crystallinity assessment revealed that comminuting efficiency of Eisenia and Eudrilus was prudent at 7 and 10 worm/kg stockings, respectively. Moreover, the 5 and 7 worm/kg stockings effectively mobilized microbial activity, promoting NPK-mineralization and C-humification balance. Correlation statistics indicated that earthworm stocking density-driven microbial community shift and fatty acid profiles strongly influenced metal removal in vermibeds. Hence, the findings implied that 5–7 worm/kg stockings of earthworms produced high-quality sanitized vermicompost.

Significant Shifts in Microbial Communities Associated with Scleractinian Corals in Response to Algae Overgrowth.

Microbes play a key role in reef dynamics, mediating the competition between scleractinian corals and benthic algae; however, major shifts in bacterial communities among coral species in response to increases in the abundance of algae are not well understood. We investigated the taxonomic composition of coral-associated microbial communities under algae-overgrowth conditions using 16S rRNA gene sequencing. The results showed that non-algal (i.e., healthy) tissue (HH) had lower bacterial abundance and diversity than tissue collected from the coral-algae interface boundary (HA) and areas of algae growth (AA). Specifically, the HA and AA samples had higher relative abundances of Saprospiraceae, Rhodobacteraceae, and Alteromonadaceae. Compared with Platygyra sp. and Montipora sp., the physiological response of Pocillopora sp. was more intense under algae-induced stress based on microbial gene function prediction. Our results indicate that algal pressure can significantly alter the microbial community structure and function of coral ecosystems. Our data thus provide new insight into the relationship between corals and their microbiome under environmental stress.