Total Microbial Abundance Research Articles

Soil microbial community development across a 32-year coastal wetland restoration time series and the relative importance of environmental factors

Soil microbes play key roles in ecosystem functioning through processes such as organic matter decomposition, nutrient and carbon cycling, and regulating vegetation structure and productivity. Coastal marshes are situated at the confluence of terrestrial and marine ecosystems; thus, their soils support abundant and diverse microbiota which facilitate globally important biogeochemical processes including nutrient cycling and greenhouse gas fluxes. With coastal marsh ecosystems threatened by relative sea level rise, subsidence, and development, mitigation for the loss of marshes is becoming commonplace. Despite the widespread implementation of marsh construction projects, little is known about the development and variability of microbial communities in created marshes. For this study, we tested the hypothesis that microbial community composition differs across created marshes of different ages and between created and natural marshes. We also hypothesized that the microbial community would be correlated with soil properties including soil organic carbon and nitrogen content, which were predicted to increase with marsh age. To test these hypotheses, we determined dominant microbial groups and environmental characteristics from six constructed marshes ranging in age from 0 to 32 years old, as well as an adjacent natural marsh. Our results revealed that microbial biomass estimates increased with marsh age except for the high elevation 20-year old marsh, yet each marsh contained a distinct microbial community composition. Across marshes, microbial community composition was significantly related to soil C:N ratio with an increase in total microbial abundance and actinomycetes and GM+ bacteria with an increase in soil C to N ratio. Additionally, shifts in dominant microbial groups were associated with differences in vegetation, elevation, and marsh age. The natural marsh community grouped more closely with younger rather than older marshes suggesting age is less important than environmental conditions. This study shows that microbial communities are not homogenized across restoration sites and do not necessarily converge to be similar to natural marshes over time. Local biotic and environmental conditions were correlated with microbial compositions, yet in seemingly similar conditions, microbial groups also differed. The effect of differences in microbial compositions on ecological functions are yet to be fully understood.

The impact of crop diversification, tillage and fertilization type on soil total microbial, fungal and bacterial abundance: A worldwide meta-analysis of agricultural sites

Microorganisms play a key role in nutrient cycling in agriculture and can contribute to improve soil quality and enhance crop production. Thus, there is a need to identify the most suitable management practices which foster increases in soil microbial biomass and diversity. A meta-analysis was performed to assess changes in microbial abundance in agricultural soils affected by: (i) management practices (tillage, fertilization and crop diversification); and (ii) environmental factors, including climate characteristics and soil properties. The scope of the meta-analysis was to evaluate whether microbial abundances are affected or not by organic fertilization or no fertilization, crop diversification (intercropping and crop rotations) and conservation tillage (reduced tillage/no-tillage) as an alternative to intensive conventional monocultures in agriculture. Only papers showing data on phospholipid fatty acids (PLFAs), providing indicators about soil microbial (total PLFA), fungal and bacterial biomass reached a critical mass to perform the meta-analysis. Therefore, soil microbial diversity could not be analyzed considering different management practices. Results showed that intercropping and crop rotations only significantly increased the abundance of fungi, with the corresponding increase in the fungal-to-bacterial ratio. Organic fertilization contributed to significant increases in bacterial and fungal abundance and total PLFA compared to mineral fertilization. Contrarily, the lack of fertilization negatively affected total PLFA, with no significant effect on bacterial and fungal abundances. Reduced tillage significantly increased total PLFA, fungal and bacterial abundances compared to conventional tillage, while no tillage had only a positive effect on fungi. Thus, as a general pattern, the adoption of sustainable management practices, mostly organic fertilization and reduced tillage, has overall positive effects on soil total microbial, fungal and bacterial abundance. These variables were not related to soil physicochemical properties and climatic factors, suggesting a positive global effect of sustainable management practices on soil microbial abundances. Thus, this study shows new insights by a meta-analysis of global studies about the effect of sustainable management practices on soil microbial abundances, needed for land-managers, policy-makers and farmers to select sustainable cropping systems that enhance microbial abundance.

Responses of Soil Microbial Community and Enzyme Activities to Shrub Species Artemisia gmelinii in Relation to Varying Rainfall in a Semiarid Land, SW China

Widely distributed shrubs in drylands can locally alter soil physicochemical properties, which distinguish soil under plant canopy from soil outside the canopy. In the present study, we used a dominant shrub species Artemisia gmelinii in a semiarid land, SW China, to investigate the consequences of “shrub resource islands” for soil microbial communities and enzymatic activities. Such investigation was made at four sites that differed in rates of rainfall to examine how the consequences were altered by variation in the local climate. The results showed that A. gmelinii enhanced fungal abundance but did not influence bacterial abundance, resulting in higher total microbial abundance and fungal-to-bacterial ratio in under-canopy soil compared to outside-canopy soil. Microbial community composition also differed between the two soils, but this difference only occurred at sites of low rainfall. Redundancy analysis revealed that such composition was attributed to variation in soil water content, bulk density, and total phosphorus as a result of shrub canopy and varying rates of rainfall. Activities of hydrolytic enzymes (β-1,4-glucosidase, β-1,4-N-acetylglucosaminidase, alkaline phosphatase, and leucine aminopeptidase) were higher in under-canopy soil than in outside-canopy soil, among which C-acquisition enzyme, β-1,4-glucosidase, and P-acquisition enzyme, alkaline phosphatase, were also higher in the soil of high rainfall. The overall pattern of enzyme activities did not show differences between under- and outside-canopy soils, but it separated the sites of high rate from that of low rates of rainfall. This pattern was primarily driven by variation in soil physicochemical properties rather than variation in soil microbial community, suggesting that the distribution pattern of enzyme activities may be more sensitive to variation in rainfall than to shrub canopy. In conclusion, our study shows that shrub species A. gmelinii can shift the soil microbial community to be fungal-dominant and increase hydrolytic enzyme activities, and such effect may depend on local climatic variation, for example, rainfall changes in the semiarid land. The findings of this study highlight the important roles of shrub vegetation in soil biological functions and the sensitivity of such roles to climatic variation in semiarid ecosystems.

Compositions of sequestrated soil carbon in constructed wetlands of Taiwan

Constructed wetlands are an ecological engineering technology that has been widely applied to treat anthropogenic wastewater. Until now, few studies have focused on soil carbon (C) in the constructed treatment wetlands in tropical regions. Therefore, this study provides insight into the changes in soil C composition of tropically constructed wetlands at different ages. Five constructed wetlands were investigated in northern Kaohsiung, Taiwan. Soil C was analyzed at three different depths using an acid-hydrolysable method. The results showed that soil TOC content was highest on the soil surface (0–2 cm) and decreased at greater soil depths (2–5 and 5–10 cm) in all the studied constructed wetlands. There was more soil acid-hydrolysable C in the older constructed wetlands than in the younger ones at all depths. On the contrary, the soil recalcitrant carbon (RP-C) did not vary much across the wetland soils. In addition, the RP-C to TOC ratios were higher in the younger than older constructed wetlands, implying that the soil bioavailable C sources for microbial growth increased with the wetland's age. As a result, the compositions of organotrophic microbes, such as methanogens (mcrA copies), appeared to increase with wetlands' ages (i.e., negatively correlated with RP-C/TOC), while the total microbial abundance (16S rDNA) and abundance of lithotrophic microbes, such as methanotrophs (pmoA copies), were not correlated with RP-C/TOC or AHPI-C/TOC ratios, based on the results of our canonical correspondence analysis. Furthermore, the constructed wetlands accumulated soil RP-C from 2.33 to 0.08 g C m−2 day−1 in the constructed wetlands 1 to 30 years old, respectively.

Optimizing cover crop and fertilizer timing for high maize yield and nitrogen cycle control

Residues of cover crop grasses release nitrogen (N) to subsequent crops, which can contribute to sustainable agricultural management and prevent increases in N-loss-related microorganisms. Moreover, applying N fertilizer to cover crops can enhance the N-use efficiency and yields of subsequent cash crops and tighten the N cycle in the soil. However, the long-term effects of N fertilization of cover crops on soil microbiota and the N cycle in tropical grass-crop no-till systems are unknown. The aim of this study was to evaluate the long-term effects of the timing of N fertilization of cover crops or maize on crop yields, total microbial abundances and N-cycle gene abundances at the time of maize harvest. We carried out a field experiment with two cover crops (palisade grass (Urochloa brizantha) and ruzigrass (U. ruziziensis) fertilized with 120 kg N ha−1 (ammonium sulfate) at one of three times: (i) broadcast over the green cover crops at 35 days before maize seeding (35 DBS), (ii) broadcast over the cover crop straw residues at 1 day before maize seeding (1 DBS), and (iii) as side-dressing at the maize V4 growth stage according to the conventional method (band-applied 0.05 m from the maize row). A control treatment without N application was also carried out for both cover crop species. Except for the control, 40 kg N ha−1 as ammonium sulfate was subsurface band-applied in all treatments 0.05–0.10 m from the maize row at maize seeding, corresponding to 160 kg N ha−1. The total bacterial, archaeal and fungal abundances and abundances of microbial genes encoding enzymes of the N cycle in the soil were quantified by real-time PCR at the maize harvest stage. Overall, maize yield increased significantly in all N fertilizer applications (average 13 Mg ha−1) compared with the control (6 Mg ha−1) over three growing seasons, with maize following palisade grass having the highest yield. The abundances of archaea and fungi in soil were highest under palisade grass that received N at 35 DBS, with values of 4.6 × 106 and 1.7 × 107 gene copies/g of dry soil, respectively. Both cover crop straw production and N release to the soil were positively correlated with the total microbe densities. When ruzigrass was the cover crop, low N enhanced nifH abundance. Archaeal amoA abundance was positively correlated with cover crop biomass and N release regardless of the N treatment and was highest under palisade grass. Bacterial amoA, nirK, and nirS abundances were highest in soil under ruzigrass and were not linked to cover crop biomass mineralization. We conclude that N fertilizer should be applied using the currently recommended method (40 and 120 kg N ha−1 at seeding and side-dressed in maize, respectively) following palisade grass to achieve high maize yield while controlling the level of N loss from tropical soil via nitrification and denitrification.

Microbial functions and soil nitrogen mineralisation processes in the soil of a cool temperate forest in northern Japan

There is little knowledge about microbial functional community structures and the relationships between microbial communities and nitrogen transformation processes. Here, we investigated the relationships between soil microbial communities and nitrogen mineralisation potentials in a cool temperate forest throughout the growing season. Microbial communities were assessed by quantification of the total bacterial, archaeal, and fungal gene abundances and the bacterial and archaeal amoA gene abundances, functional predictions of bacteria and fungi, and analysis of the bacterial-fungal co-occurrence network. In mid-summer, ectomycorrhizal fungal abundance was significantly higher, whereas the total bacterial abundance was significantly lower. Bacterial and archaeal amoA gene abundances were also significantly higher in mid-summer. However, regardless of the seasonal fluctuation of microbial gene abundances, the net nitrification and nitrogen mineralisation potential did not show clear seasonality. In the network analysis, the microbial community was divided into 13 modules, which were subgroups assumed to have similar niches. Furthermore, two modules that mainly consisted of microbial species of Proteobacteria and Bacteroidetes were significantly and positively correlated with the net nitrification and mineralisation potentials. Our results indicated that microbial subgroups sharing similar niches, instead of total microbial abundances and functional gene abundances, could be important factors affecting the net nitrogen mineralisation potential.

Composition change and decreased diversity of microbial eukaryotes in the coastal upwelling waters of South China Sea

Upwelling plays an important role in marine ecosystems and potentially reshapes microbial communities by enhanced dispersal and distinct environmental drivers. Relative to that of bacterioplankton, however, the response of eukaryotic microbes to upwelling is largely unknown. Here, we investigated the influence of coastal upwelling in South China Sea on the microbial eukaryotic communities. Unlike several folds of increase in the cell abundance of bacterioplankton in upwelling than non-upwelling stations at corresponding water layers, no significant difference was detected for the total microbial eukaryotic 18S rRNA gene abundance. Moreover, the microbial eukaryotes in the upwelling stations exhibited increasing 18S rRNA gene abundance from the surface to the deep, contrasting the vertical cell abundance pattern of the bacterioplankton; but their vertical abundance patterns were similar in non-upwelling stations. Importantly, the coastal upwelling significantly reduced the community evenness of the microbial eukaryotes and slightly reduced their Shannon diversity. Their community composition also varied obviously especially between the surface waters of upwelling and non-upwelling stations. Among the dominant supergroups, Alveolata was found to be less abundant while Stramenopiles, particularly thraustochytrids and diatoms, to be more abundant in the surface water of upwelling than non-upwelling stations. Temperature was identified as the most important factor of the microbial eukaryotic community composition, suggesting potential effects of the cold upwelling water masses on specific taxa. Overall, our results reveal significant and distinct impacts of coastal upwelling on the abundance, diversity, and community structure of microbial eukaryotes, filling the knowledge gap about the microbial responses to this important marine phenomenon.

Short-term impact of fire on the total soil microbial and nitrifier communities in a wet savanna.

Savannas are characterized by the coexistence of grasses and trees. Fires are critical for their coexistence, because they decrease the survival of tree seedlings and saplings and their recruitment to the adult stage. In some humid savannas, perennial grasses inhibit nitrification and trees stimulate nitrification, which likely favors coexistence between trees and grasses. However, fires may influence plant capacity to control nitrogen cycling, which could subsequently influence tree–grass coexistence and savanna nitrogen budget. Therefore, we sampled soil in a humid savanna of Ivory Coast under the dominant nitrification‐inhibiting grass species and the dominant nitrification‐stimulating tree species and under bare soil before and after (i.e., 5 days) fire during the long dry season. We quantified the total microbial and nitrifier abundances and transcriptional activities and the nitrification enzyme activity. Fire decreased soil water content, probably by increasing evaporation and, maybe, by triggering the growth of grasses, and increased soil ammonium availability likely due to ash deposition and increased mineralization. Fire did not impact the total archaeal, bacterial, or fungal abundances, or that of the nitrifiers. Fire did not impact archaeal transcriptional activity and increased bacterial and fungal total transcriptional activities. In contrast, fire decreased the archaeal nitrifier transcriptional activities and the nitrification enzymatic activity, likely due to the often reported resumption of the growth of nitrification‐inhibiting grasses quickly after the fire (and the subsequent increase in root exudation). These results pave the way for a better understanding of the short‐term effects of fire on nitrogen cycling and tree–grass competition for nitrogen.

Scavenging beetles control the temporal response of soil communities to carrion decomposition

Abstract Carrion is a frequent but overlooked source of nutrients to the soil. The decomposition of carrion is accelerated by invertebrate scavengers, but the impact of the scavengers on below‐ground biota and its functions is scarcely known. We conducted a laboratory experiment to investigate the effects of the burying beetle Nicrophorus vespilloides on the soil community of a temperate broadleaved forest. We assembled microcosms from soil collected from an oak woodland and treated them with mouse Mus musculus carcasses and mating pairs of burying beetles (♀+♂) in a factorial design with control soils. We sampled independent replicates over time to investigate how the beetles affect soil microarthropods and microbial biomass (bacteria and fungi) in relation to soil pH and organic matter content. The beetle treatment initially reduced the total microbial biomass and abundance of major groups of microarthropods relative to the control soil. At the same time, organic matter increased in the beetle treatment and then dropped to the pre‐beetle level (i.e. soil baseline) at the end of the beetle breeding cycle (2 weeks). The rapid temporal changes in organic matter were mimicked by the relative abundances of the dominant microarthropod groups, with Oribatida relatively more abundant than Collembola and predaceous mites in the beetle treatment. The overall final effect of the beetle (relative to the laboratory control) on microarthropods was negative but the beetle kept these variables within the levels observed for freshly collected soil (baseline), while the final effect on pH was positive, and most likely driven by the surplus of nutrients from the carcass and biochemical changes triggered by the decomposition process. In nature, scavenging invertebrates are widespread. Our study demonstrates that beetles breeding in carcasses regulate the dynamics of key components of the soil food web, including microbial biomass, changes in the relative abundances of dominant microarthropods and soil organic matter and pH. Given the abundance of these beetles in nature, the study implies that the distribution of these beetles is a key driver of variation in soil nutrient cycling in woodlands. A free Plain Language Summary can be found within the Supporting Information of this article.

Forage Species Identity Shapes Soil Biota in a Temperate Agroecosystem

Increasing plant diversity in the perennial phase of pasture-crop rotations is predicted to positively affect belowground productivity and microbial communities and, in turn, augment belowground agroecosystem services including soil health and carbon storage. Using two grass and one legume forage species grown as monocultures and combined in four intercropped combinations, we evaluated how species identity and richness influence belowground productivity, soil microbial communities, and soil C pools. Though grass-legume intercrops demonstrated higher aboveground productivity than component species grown in monoculture, higher species richness was not associated with increased productivity belowground. Root biomass was greatest in tall fescue (Festuca arundinacea Schreb.) monoculture, and intercrops including this species. Species identity was similarly associated with soil microbial community attributes. Orchardgrass (Dactylis glomerata L.) monoculture exhibited lower total microbial abundance and lower bacterial abundance than grass-legume intercrops. Bacterial abundance was also lower in orchardgrass compared to white clover (Trifolium repens L.) monoculture. A common indictor of soil function, the fungal:bacterial ratio, was higher in grass-only than clover-only stands. The prevalence of species-specific impacts on roots and microbial communities in this study suggests that species identity may have a stronger influence than species richness on belowground agroecosystem services from perennial forages in temperate regions.

Equivolumetric Protocol Generates Library Sizes Proportional to Total Microbial Load in 16S Amplicon Sequencing.

High-throughput sequencing of 16S rRNA amplicon has been extensively employed to perform microbiome characterization worldwide. As a culture-independent methodology, it has allowed high-level profiling of sample bacterial composition directly from samples. However, most studies are limited to information regarding relative bacterial abundances (sample proportions), ignoring scenarios in which sample microbe biomass can vary widely. Here, we use an equivolumetric protocol for 16S rRNA amplicon library preparation capable of generating Illumina sequencing data responsive to input DNA, recovering proportionality between observed read counts and absolute bacterial abundances within each sample. Under specified conditions, we show that the estimation of colony-forming units (CFU), the most common unit of bacterial abundance in classical microbiology, is challenged mostly by resolution and taxon-to-taxon variation. We propose Bayesian cumulative probability models to address such issues. Our results indicate that predictive errors vary consistently below one order of magnitude for total microbial load and abundance of observed bacteria. We also demonstrate our approach has the potential to generalize to previously unseen bacteria, but predictive performance is hampered by specific taxa of uncommon profile. Finally, it remains clear that high-throughput sequencing data are not inherently restricted to sample proportions only, and such technologies bear the potential to meet the working scales of traditional microbiology.

Three antimicrobials alter gut microbial communities and causing different mortality of brown planthopper, Nilaparvata lugens Stål

The symbionts in the gut of brown planthopper play an important role in the nutrition utilization and growth of their host, Nilaparvata lugens Stål (Hemiptera: Delphacidae). Controlling the BPH infection on rice by inhibiting the symbionts using antimicrobials is feasible. However, the impact of antimicrobials on the microbiome in the gut has not been fully elucidated. In this study, we found the mortality reached 35.5%, 33.1% and 19.4%, when BPHs were exposed to toyocamycin, tebuconazole, and zhongshengmycin, respectively. Significant differences were found between the structures of gut microbial communities in adult BPHs treated with different antimicrobials and water. The antimicrobials reduced the fungal diversity by reducing the non-dominant fungi abundance, and increased bacterial diversity by inhibiting the dominant bacteria Acinetobacter in the gut. The diversification of taxonomic groups in gut depended on the different selective stress of antimicrobials. For the microbial absolute abundance, the total microbial gut community abundance decreased under antimicrobial exposure, but the absolute abundance of Serratia significantly increased in the antimicrobial treatment group. Overall, our study enriched the knowledge of microbiomes in the gut of BPH under the antimicrobial treatment and provided guidelines to enhance the pest management effect of BPH by using antimicrobials.

Bioaugmentation strategy to enhance polycyclic aromatic hydrocarbons anaerobic biodegradation in contaminated soils

This paper proposes an innovative bioaugmentation approach for the remediation of polycyclic aromatic hydrocarbon (PAH) contaminated soils, based on a novel habitat-based strategy. This approach was tested using two inocula (i-24 and i-96) previously enriched through an anaerobic digestion process on wheat straw. It relies on the application of allochthonous microorganisms characterized by specific functional roles obtained by mimicking a natural hydrolytic environment such as the rumen. The inocula efficiency was tested in presence of naphthalene alone, benzo[a]pyrene alone, and a mix of both of them. In single-contamination tests, i-24 inoculum showed the highest biodegradation rates (84.7% for naphthalene and 51.7% for benzo[a]pyrene). These values were almost 1.2 times higher than those obtained for both contaminants with i-96 inoculum and in the control test in presence of naphthalene alone, while they were 3 times higher compared to the control test in presence of benzo[a]pyrene alone. In mixed-contamination tests, i-96 inoculum showed final biodegradation efficiencies for naphthalene and benzo[a]pyrene between 1.1 and 1.5 higher than i-24 inoculum or autochthonous biomass. Total microbial abundances increased in the bioaugmented tests in line with the PAH degradation. The microbial community structure showed the highest diversity at the end of the experiment in almost all cases. Values of the Firmicutes active fraction up to 7 times lower were observed in the i-24 bioaugmented tests compared to i-96 and control tests. This study highlights a successful bioaugmentation strategy with biological components that can be reused in multiple processes supporting an integrated and environmentally sustainable bioremediation system.

Temporal fluctuations of microbial communities within the crop growing season

Soil microbial communities maintain many ecosystem functions including decomposition and symbiotic nutrient uptake. Prior field studies have focused on either geospatial or relatively large-time scale trends in these communities. Whereas, their small-time scale (e.g., weekly) dynamics in agricultural fields have largely been overlooked. Our objective was to determine the effects and characteristics of short-time scales on five phospholipid fatty acid (PLFA) microbial groups throughout the whole growing season, while under two soil disturbance levels. The microbial community groups included total microbial abundance (TMA), arbuscular mycorrhizal fungi (AMF), total fungi, actinomycetes, and total bacteria. The fungal to bacterial ratio (F:B) was also determined. Soils were sampled twice per week from planting to harvest during two consecutive growing seasons (N = 62) and analyzed for microbial abundances and chemical and physical properties. The study was conducted at an on-farm site with a corn [Zea mays] – soybean [Glycine max] – wheat [Triticum aestivum] rotation and two soil disturbance levels [high (chisel plow) and low (shallow vertical till)] using a randomized complete block design. Data analysis included 1) spatial and temporal coefficients of variations, 2) a mixed linear model to test for time and disturbance level effects, and 3) a Fourier analysis to detect and characterize cyclical patterns via autocorrelation spectral densities. The Fourier analysis also included cross spectral densities and phase lags with a large suite of soil chemical, soil physical, and weather states. Temporal variations of microbial communities were one to threefold greater than their spatial variations. Significant time effects were observed for TMA, AMF, and bacteria, where these communities behaved as sine and consine functions over time. However, strong cyclical patterns were above white noise levels at the experimental plots level for all microbial groups during each growing season. Cross spectral densities indicated that bacteria and actinomycetes tended to cycle at short and long periods (biweekly to whole season) associated with soil physical and weather states, whereas TMA, AMF, fungi, and F:B cycles at long periods (bimonthly to whole season) associated with soil chemical states. These microbial communities in a field setting clearly undergo cyclical patterns over small periods with some modulations from soil disturbance levels, fertilization, and microtopography. Further research on these cyclical and cross-correlated dynamics is warranted to determine the magnitude of influence on ecosystem services and crop productivity.

Decline in Soil Microbial Abundance When Camelina Introduced Into a Monoculture Wheat System.

Camelina [Camelina sativa (L.) Crantz] of the Brassicaceae family is a potential alternative and oilseed biofuel crop for wheat (Triticum aestivum L.)-based cropping systems of the Inland Pacific Northwest (PNW) of the United States. We investigated the effect of this relatively new rotational crop on soil microbial communities. An 8-year cropping systems experiment was initiated in 2007 at Lind, WA, to compare a 3-year rotation of winter wheat (WW)-camelina (C)-fallow (F) to the typical 2-year WW-F rotation. All phases of both rotations (total = 20 plots) were present every year to allow valid statistical analysis and data interpretations. Monoculture WW-F is the dominant system practiced by the vast majority of farmers on 1.56 million ha of cropland in the PNW drylands that receive <300 mm average annual precipitation. Microbial abundance and community composition were determined using phospholipid fatty acid analysis (PLFA) from soil samples collected during 3 consecutive years beginning in 2010. The abundance of fungi, mycorrhizae, Gram positive and negative bacteria, and total microbial abundance all declined over the 3-year period in the WW-C-F rotation compared to the WW-F rotation. All microbial lipid biomarkers were significantly less in fallow compared to WW of the WW-C-F rotation. The 2-year WW-F rotation demonstrated few differences in microbial lipid abundance and community structure between the rotation phases. Microbial abundance declined and community structure shifted in the 3-year WW-C-F rotation likely due to the combination of a Brassica crop followed by a 13-month-long fallow. The results of this study suggest that camelina in combination with a fallow period may disrupt microbial communities that have become stable under historical WW-F monocropping. Such disturbances have the potential to affect soil processes that have been provided by wheat-adapted microbial communities. However, the disruption appears to be short-lived with the microbial abundance of WW in the WW-C-F rotation, returning to similar levels observed in the WW-F rotation.

Potential complementary functions among bacteria, fungi, and archaea involved in carbon cycle during reversal of desertification

AbstractDevelopment of biological soil crusts (BSCs) on bare land is a sign of reversal of desertification, and microbial communities of BSCs are the biogeochemical engineers of desert ecosystems. However, regulation of different microbial groups involved in the carbon (C) cycle is not clear. This study investigated the correlation between bacteria, fungi, and archaea of BSCs involved in the C cycle during reversal of desertification through community abundance analysis by quantitative PCR and functional gene detection using GeoChip 5.0. Among the known C cycle genes found in BSCs, 84.5% of C degradation genes, 95% of C fixation genes, and all of methane oxidation genes were derived from bacteria owing to their highest proportion among the total microbial abundance of BSCs; some recalcitrant C degradation genes were derived from fungi; and other C fixation pathway and methanogenesis genes originated from archaea. The increased abundance of bacteria and fungi and decreased abundance of archaea during reversal of desertification, as well as the difference in C cycle genes of the three microbial groups, indicated the functional complementarity among these microorganisms involved in C cycle. At the early stage of BSC development, archaea, and bacteria provide available C sources by autotrophic CO2 fixation pathway; bacteria play important roles in C degradation, C fixation, and methane oxidation during the entire BSC development process; and fungi mainly degrade lignin at the later stage of BSC development. Thus, cooperation among BSC microflora altered C cycle during reversal of desertification.

Microbial Processes and Microbial Communities in the Water Column of the Polar Meromictic Lake Bol'shie Khruslomeny at the White Sea Coast.

Microbiological, molecular ecological, biogeochemical, and isotope geochemical research was carried out at the polar Lake Bol’shie Khruslomeny at the coast of the Kandalaksha Bay, White Sea in March and September 2017. The uppermost mixolimnion was oxic, with low salinity (3–5%). The lower chemocline layer was brown-green colored, with very high content of particulate organic matter (up to 11.8 mg C L–1). The lowermost monimolimnion had marine salinity (22–24%) and very high concentrations of sulfide (up to 18 mmol L–1) and CH4 (up to 1.8 mmol L–1). In the chemocline, total microbial abundance and the rate of anoxygenic photosynthesis were 8.8 × 106 cells mL–1 and 34.4 μmol C L–1 day–1, respectively. Both in March and September, sulfate reduction rate increased with depth, peaking (up to 0.6–1.1 μmol S L–1 day–1) in the lower chemocline. Methane oxidation rates in the chemocline were up to 85 and 180 nmol CH4 L–1 day–1 in March and September, respectively; stimulation of this process by light was observed in September. The percentages of cyanobacteria and methanotrophs in the layer where light-induced methane oxidation occurred were similar, ∼2.5% of the microbial community. Light did not stimulate methane oxidation in deeper layers. The carbon isotope composition of particulate organic matter (δ13C-Corg), dissolved carbonates (δ13C-DIC), and methane (δ13C- CH4) indicated high microbial activity in the chemocline. Analysis of the 16S rRNA gene sequences revealed predominance of Cyanobium cyanobacteria (order Synechococcales) in the mixolimnion. Green sulfur bacteria Chlorobium phaeovibrioides capable of anoxygenic photosynthesis constituted ∼20% of the chemocline community both in March and in September. Methyloprofundus gammaptoteobacteria (family Methylomonaceae) were present in the upper chemocline, where active methane oxidation occurred. During winter, cyanobacteria were less abundant in the chemocline, while methanotrophs occurred in higher horizons, including the under-ice layer. Chemolithotrophic gammaproteobacteria of the genus Thiomicrorhabdus, oxidizing reduced sulfur compounds at low oxygen concentrations, were revealed in the chemocline in March. Both in March and September archaea constituted up to 50% of all microorganisms in the hypolimnion. The percentage of putative methanogens in the archaeal community was low, and they occurred mainly in near-bottom horizons.

Si-induced DMA desorption is not the driver for enhanced DMA availability after Si addition to flooded soils

Silicon (Si) addition to flooded rice paddy soil tends to decrease grain inorganic arsenic (iAs) and increase grain dimethylarsinic acid (DMA) concentrations, but the mechanism for the increase in plant-available DMA is unresolved. It has been suggested that Si displaces DMA from soil solids, rendering it plant-available; however, we hypothesize that Si desorbs primarily iAs from soil solids, which stimulates methylation to DMA. We added silicic acid to a contaminated paddy soil and a flooded upland soil that had been historically contaminated with lead arsenate in a batch incubation experiment, and measured changes in solid-phase As speciation, porewater As speciation, and As-methylating microbial (AsMM) abundance over time. We found that DMA was not detectable in soils prior to the start of the experiment nor throughout the experiment, so it comprised a trace amount of total soil As. Upon Si addition to paddy soil, total As increased in porewater following Si spike and this increase was mainly due to iAs desorption, and an order of magnitude less MMA and DMA was desorbed. The upland soil transitioned to reducing conditions throughout the experiment, but when they were achieved, iAs was desorbed first and this was followed by an increase of MMA and then DMA compared to control soils. Total microbial community abundance increased over the course of the experiments and arsM gene abundance increased from initial conditions, but did not differ between treatments. In the paddy soil, the ratio of arsM:16S gene abundance decreased from the initial conditions, but it increased in the upland soil with historic As contamination. These results suggest that Si-induced desorption of DMA is small and likely does not explain the increases of plant-available DMA upon Si fertilization in prior work. Likely, Si-induced iAs desorption drives microorganisms to methylate iAs, but degree of methylation will differ between soils.

Linking Human Milk Oligosaccharides, Infant Fecal Community Types, and Later Risk To Require Antibiotics.

Human milk oligosaccharides (HMOs) may provide health benefits to infants partly by shaping the development of the early-life intestinal microbiota. In a randomized double-blinded controlled multicentric clinical trial, healthy term infants received either infant formula (control) or the same formula with two HMOs (2'-fucosyllactose and lacto-N-neotetraose; test) from enrollment (0 to 14 days) to 6 months. Then, all infants received the same follow-up formula without HMOs until 12 months of age. Breastfed infants (BF) served as a reference group. Stool microbiota at 3 and 12 months, analyzed by 16S rRNA gene sequencing, clustered into seven fecal community types (FCTs) with marked differences in total microbial abundances. Three of the four 12-month FCTs were likely precursors of the adult enterotypes. At 3 months, microbiota composition in the test group (n = 58) appeared closer to that of BF (n = 35) than control (n = 63) by microbiota alpha (within group) and beta (between groups) diversity analyses and distribution of FCTs. While bifidobacteriaceae dominated two FCTs, its abundance was significantly higher in one (FCT BiH for Bifidobacteriaceae at high abundance) than in the other (FCT Bi for Bifidobacteriaceae). HMO supplementation increased the number of infants with FCT BiH (predominant in BF) at the expense of FCT Bi (predominant in control). We explored the association of the FCTs with reported morbidities and medication use up to 12 months. Formula-fed infants with FCT BiH at 3 months were significantly less likely to require antibiotics during the first year than those with FCT Bi. Previously reported lower rates of infection-related medication use with HMOs may therefore be linked to gut microbiota community types. (This study has been registered at ClinicalTrials.gov under registration number NCT01715246.)IMPORTANCE Human milk is the sole and recommended nutrition for the newborn infant and contains one of the largest constituents of diverse oligosaccharides, dubbed human milk oligosaccharides (HMOs). Preclinical and clinical association studies indicate that HMOs have multiple physiological functions largely mediated through the establishment of the gut microbiome. Until recently, HMOs were not available to investigate their role in randomized controlled intervention trials. To our knowledge, this is the first report on the effects of 2 HMOs on establishing microbiota in newborn infants. We provide a detailed description of the microbiota changes observed upon feeding a formula with 2 HMOs in comparison to breastfed reference infants' microbiota. Then, we associate the microbiota to long-term health as assessed by prescribed antibiotic use.

Native Bamboo Invasions into Subtropical Forests Alter Microbial Communities in Litter and Soil

Both exotic and native plant invasions can have profound impacts on ecosystems. While many studies have examined the effects of exotic plant invasions on soil properties, relatively few have tested the effects of native plant invasions on soil microbial communities. Furthermore, we know little about the effects of native plant invasions on microbial communities in litter. In subtropical forests in southern China, we sampled litter at three decomposition stages and top soil in three forest sands representing three stages of the invasion (not invaded, moderately and heavily invaded) by the Moso bamboo (Phyllostachys edulis (Carriere) J. Houzeau), a native species in China. We measured chemical properties (concentrations of C, N, P, Mg, Al, K, Ca, Mn, Cu, and Zn, and concentrations of cellulose and lignin) and microbial communities in litter and/or soil. The bamboo invasion, in general, decreased the element concentrations in litter and soil and also decreased total microbial abundance and diversity. Considering bacteria and fungi separately, the bamboo invasion decreased fungal diversity in litter and soil, but had little impact on bacterial diversity, suggesting that fungi are more sensitive and vulnerable to the bamboo invasion than bacteria. We conclude that native Moso bamboo invasions into subtropical forests may lead to a complex biogeochemical process in the litter–soil system, which may threaten local forest ecosystems by affecting microbial communities and, thus, litter decomposition and nutrient cycling.