Total Microbial Biomass Research Articles

Changes of microbial community and activity under different electric fields during electro-bioremediation of PAH-contaminated soil

Electro-bioremediation is a promising technology for remediation of soil contaminated with persistent organic compounds such as polycyclic aromatic hydrocarbons (PAHs). During electro-bioremediation, electrical fields have been shown to increase pollutant degradation. However, it remains unclear whether there is an optimal strength for the electrical field applied that is conductive to the maximum role played by microbes. This study aimed to determine the optimal strength of electric field through the analysis of the effects of different voltages on the microbial community and activity. Four bench-scale experiments with voltages of 0, 1, 2 and 3 V cm−1 were conducted for 90 days in an aged PAH-contaminated soil. The spatiotemporal changes of the soil pH, moisture content and temperature, microbial biomass and community structure, and the degradation extent of PAHs were researched over 90 days. The results indicated that the total microbial biomass and degradation activity were highest at voltages of 2 V cm−1. The concentration of total phospholipid fatty acids, used to quantify soil microbial biomass, reached 65.7 nmol g−1 soil, and the mean degradation extent of PAHs was 44.0%. Similarly, the maximum biomass of actinomycetes, bacteria and fungus also occurred at the voltage of 2 V cm−1. The Gram-positive/Gram-negative and (cy17:0+cy 19:0)/(16:1ω7+18:1ω7) ratios also showed that the intensity of electric field and electrode reactions strongly influenced the microbial community structure. Therefore, to optimize the electro-bioremediation of PAH-contaminated soil, the strength of electric field needs to be selected carefully. This work provides reference for the development of novel electrokinetically enhanced bioremediation processes.

Responses of Soil Microbial Community Composition and Enzyme Activities to Land-Use Change in the Eastern Tibetan Plateau, China

The land-use change is a major determinant influencing ecosystem carbon (C) patterns and nutrient cycling in subalpine forests in the Eastern Tibetan Plateau. While some results have been obtained in relation to the influence of land-use change on aboveground components, less is known about the belowground microbial communities and related processes. We assessed the structure and function of soil microbial communities following land-use change from old-growth forest (OF) to secondary forest (SF), plantation forest (PF), and grassland (GL) in the Eastern Tibetan Plateau, China. Phospholipid fatty acid profiles and enzyme activity analysis were used to determine the composition and activities of microbial communities, respectively. Significant differences in physicochemical characteristics, microbial communities, and extracellular enzyme activities in soils under different land uses were observed in this study. pH and total nitrogen (TN) in OF and SF were significantly higher than in GL. PF showed the highest soil organic C (SOC), and significantly higher than in GL. Total phosphorus (TP) and C/N ratio in PF were significantly higher than the other land-use types. OF and PF had significantly higher anaerobic bacteria than in GL. The actinobacteria in SF was significantly higher than in PF. The saprotrophic and ectomycorrhizal (SEM) fungi was significantly lower in GL than the other land-use types. Total microbial biomass and β-glucosidase activities were significantly higher in OF and SF than in GL. GL had significantly higher polyphenoloxidase activities than in OF and PF. Anaerobic bacteria, arbuscular mycorrhizal fungi and SEM fungi were positively correlated with SOC and TP, Gram+ bacteria were correlated with C/P and N/P ratio. N-acetylglucosaminidase activity was negatively correlated with anaerobic bacteria, while polyphenoloxidase activity was positively related to actinobacteria. Furthermore, redundancy analysis revealed that the microbial community composition was primarily regulated by TN and pH. This suggested that altered land-use type initiated changes in the physicochemical characteristics of the soils, which affected the composition of microbial communities and microbial enzyme activities related to nutrient cycling in this area. This provides a scientific basis for the influence mechanism of land use on composition and function of microbial communities, as well as the rational utilization and management of land resources.

Drought stress induced increase of fungi:bacteria ratio in a poplar plantation

Soil microbial communities are key to ecosystem processes in terrestrial ecosystems. Although droughts are projected to be more frequent with the intensifying effects of climate change, our understanding of the responses of soil microbial communities to drought remains incomplete. For this study, we employed 30% and 50% throughfall reduction manipulation experiments to simulate different drought intensities, and collected soil samples at three depths (0–15, 15–30 and 30–45 cm) for each season in a poplar plantation. We analyzed the physical and chemical properties of the soil samples (e.g., soil moisture, pH, total C, total N, and labile organic C and N contents represented by extractable organic C and N contents, microbial biomass C and N contents) and microbial communities, via phospholipid fatty acid (PLFA) and high-throughput sequencing methods, from November 2018 to August 2019. We found that drought significantly decreased soil moisture, the content of soil labile organic C and N, and total microbial biomass; however, it increased soil pH and microbial biomass C:N across all soil depths. Furthermore, fungi:bacteria and Gram+:Gram- bacterial ratios increased with drought treatments across all three soil depths. Drought reduced the relative abundance of Proteobacteria, but increased the relative abundance of Acidobacteria across the three soil depths. In contrast, drought had no significant influence on the relative abundance of fungal phyla. The changes in soil properties and microbial communities increased with drought intensity. Regression analysis demonstrated that changes in the total PLFA, fungi:bacteria and Gram+:Gram- bacterial ratios were significantly correlated with soil moisture, pH, and the soil labile organic C and N content. Redundancy analysis revealed that soil pH, extractable organic C and extractable organic N accounted for the majority of the variabilities in the bacterial communities. The patterns of fungal community structures in the drought treatment plots were not distinct from the control groups across three soil depths. Our results suggested that droughts induce significant increases in fungi:bacteria and Gram+:Gram- bacterial ratios in forest soils, primarily through changes in soil pH, moisture, and soil labile organic C and N content.

Response of soil microbial communities to additions of straw biochar, iron oxide, and iron oxide-modified straw biochar in an arsenic-contaminated soil.

Anthropogenic activities have caused extensive arsenic (As) contamination in soils. The role of biochar in the remediation of As-contaminated soils has been attracting attention lately. In this study, effects of straw biochar, iron oxide, and iron oxide-modified biochar on soil microbial community composition and soil chemical properties were tested in an As-contaminated soil. After 9months of incubation, soil chemical properties and microbial communities were analyzed. Our results showed that biochar addition significantly increased soil pH value, soil organic carbon (SOC) concentration, and the ratio of soil carbon to nitrogen (soil C:N ratio) but decreased soil dissolved organic C. Adding iron oxide also increased soil pH value, while iron oxide-modified biochar decreased it. Interestingly, compared with the control, all treatments significantly decreased soil total microbial biomass and biomasses of soil bacteria, fungi, Actinomyces, and protozoa. In addition, significantly positive correlations were found between soil pH and soil total microbial biomass as well as bacterial, Actinomyces, and arbuscular mycorrhizal fungal biomass. There were negative relationships between SOC, soil C:N ratio, and all soil microbial biomass indicators in all treatments. These results indicated that biochar and iron oxide-modified biochar affected soil microbial community composition by altering the soil C:N ratio, but iron oxide affected it via adjusting soil pH. Furthermore, the iron oxide-modified biochar effects on soil microbial community and soil chemical properties are not the same as the additive effects of biochar and iron oxide alone, and its effect on soil microbial community is regulated by the soil C:N ratio. These findings will help guide the development of remediation practices for As-contaminated soil using biochar.

Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA.

Aquifers, which are essential underground freshwater reservoirs worldwide, are understudied ecosystems that harbor diverse forms of microbial life. This study investigated the abundance and composition of prokaryotic and viral communities in the outflow of five springs across northern Florida, USA, as a proxy of microbial communities found in one of the most productive aquifers in the world, the Floridan aquifer. The average abundances of virus-like particles and prokaryotic cells were slightly lower than those reported from other groundwater systems, ranging from 9.6 × 103 ml-1 to 1.1 × 105 ml-1 and 2.2 × 103 ml-1 to 3.4 × 104 ml-1, respectively. Despite all of the springs being fed by the Floridan aquifer, sequencing of 16S rRNA genes and viral metagenomes (viromes) revealed unique communities in each spring, suggesting that groundwater microbial communities are influenced by land usage in recharge zones. The prokaryotic communities were dominated by Bacteria, and though the most abundant phyla (Proteobacteria, Cyanobacteria, and Bacteroidetes) were found in relatively high abundance across springs, variation was seen at finer taxonomic resolution. The viral sequences were most similar to those described from other aquatic environments. Sequencing resulted in the completion of 58 novel viral genomes representing members of the order Caudovirales as well as prokaryotic and eukaryotic single-stranded DNA (ssDNA) viruses. Sequences similar to those of ssDNA viruses were detected at all spring sites and dominated the identifiable sequences at one spring site, showing that these small viruses merit further investigation in groundwater systems.IMPORTANCE Aquifer systems may hold up to 40% of the total microbial biomass on Earth. However, little is known about the composition of microbial communities within these critical freshwater ecosystems. Here, we took advantage of Florida's first-magnitude springs (the highest spring classification based on water discharge), each discharging at least 246 million liters of water each day from the Floridan aquifer system (FAS), to investigate prokaryotic and viral communities from the aquifer. The FAS serves as a major source of potable water in the Southeastern United States, providing water for large cities and citizens in three states. Unfortunately, the health of the FAS and its associated springs has declined in the past few decades due to nutrient loading, increased urbanization and agricultural activity in aquifer recharge zones, and saltwater intrusion. This is the first study to describe the prokaryotic and viral communities in Florida's first-magnitude springs, providing a baseline against which to compare future ecosystem change.

Carbon Organic Content under Organic and Conventional Paddy Field and its Effect on Biological Activities (A Case Study in Pati Regency, Indonesia)

The low organic matter content of paddy soils impacts the declining quality of land. Without the efforts to enrich the soil organic matter (SOM) content, the productivity of paddy fields will decrease or the need for inorganic fertilizers will increase to reach the level of yield. The present research aims to determine the effect of differences in organic and conventional paddy fields management practices on soil organic carbon (SOC) content and biological activities. The research was conducted from July to September 2018 on organic and conventional paddy fields in Dukuhseti Sub-district, Pati Regency, Central Java, Indonesia. Sampling points were taken from six organic samples in the organic paddy fields while the other six samples were taken from conventional paddy fields. The variables observed in this research were organic C, pH, total N soil, total bacterial colonies, soil respiration and microbial biomass C. The results show that the organic C content in the organic paddy field (2.4%) was higher than that of the conventional paddy field (1.8%). The C content of organic paddy fields increased by 0.6%. The differences of the total bacterial colonies, soil respiration and microbial biomass C between organic paddy fields and conventional paddy fields were 11.5 CFU g<sup>-1</sup>, 7.42 mg CO<sub>2</sub> week<sup>-1</sup> and 0.51 µg g<sup>-1</sup>, respectively, because the use of organic farming systems could improve the biological nature of soils and caused biological activity in organic paddy fields to have the highest value compared to conventional paddy fields.

Effect of molasses based multi-nutrient herbal supplements on in vitro digestibility, serum enzymes and minerals profile in buffalo calves

Molasses based multinutrients herbal supplements (MMS) containing ground fenugreek seed and de-oiled mahua seed cake at two different ratios (1:1; MMS I or 1:3; MMS II) was evaluated under in vitro as well as in vivo conditions. For in vitro evaluation, concentrate mixture and wheat straw in 50: 50 ratio (on DM basis) was taken as substrate for the experiment. MMS I and MMS II were added at 2, 3 and 4% of the substrate, respectively. The total gas production (ml/g DM), partitioning factor (PF) and microbial biomass production (MBP) were found comparable in all the groups but significantly improved the IVDMD and IVOMD in supplemented groups. Under in vivo feeding trial, serum enzymes and minerals profile in buffalo calves were assessed during 9 months of experimental period. Fifteen male Murrah buffalo calves (10 to 15 months of age and mean body wt. 234.0±12.5 kg) were randomly distributed into 3 groups (5 in each group) according to randomized block design. All animals were fed with conventional concentrate mixture, available chopped green fodder (3-4 kg DM/d) and wheat straw ad lib to meet out nutrients requirement. While control group (C) were not fed supplements but groups T1 and T2 supplemented with MMS I and MMS II, respectively at 44 g/100 kg body weight or 200 g/100 kg metabolic body weight (kgW0.75). Serum AST, ALT activities and serum concentration of Ca, P, Fe, Mn, Cu and Co were comparable among 3 groups but serum concentration of Zn was significantly higher among supplemented groups. Thus, results show that supplementation of MMS improved IVDMD, IVOMD and serum Zn level resulting in to better health conditions of buffalo calves.

Long‐term perennial management and cropping effects on soil microbial biomass for claypan watersheds

AbstractSustainable vegetative management plays a significant role in improving soil quality in degraded agricultural landscapes by enhancing soil microbial biomass. This study investigated the effects of grass buffers (GBs), biomass crops (BCs), grass waterways (GWWs), and agroforestry buffers (ABs) on soil microbial biomass and soil organic C (SOC) compared with continuous corn (Zea mays L.)–soybean [Glycine max (L.) Merr.] rotation (row crop [RC]) on claypan soils. The RC, AB, GB, GWW, and BC treatments were established in 1991, 1997, 1997, 1997, and 2012, respectively, and are located at Greenley Memorial Research Center in Missouri. Soil samples were collected in May 2018 from the 0‐ to 10‐cm depth at summit, backslope, and footslope landscape positions. Within AB treatment, soils were collected from the 50‐cm and 150‐cm tree distance. Total microbial biomass and biomass of gram‐positive bacteria, gram‐negative bacteria, actinomycetes, rhizobia, fungi, arbuscular mycorrhizae, saprophytes, and protozoa were determined by phospholipid fatty acid (PLFA) analysis. Results showed that soil microbial biomass and SOC across all microbial groups were significantly higher (P < .01) under perennial vegetation treatments compared with RC. The footslope position exhibited the highest total microbial biomass compared with the summit and backslope positions. The sampling distance of 50 cm from the tree base demonstrated 16% greater total microbial biomass and 15% higher SOC compared with 150 cm. These findings highlight the influence of landscape on soil biological properties and show that perennial vegetation systems have the potential to increase soil microbial biomass and enhance agricultural sustainability in degraded RC systems.

Responses of soil microbes and their interactions with plant community after nitrogen and phosphorus addition in a Tibetan alpine steppe

Nitrogen (N) and phosphorus (P) additions are the widely used restoration management for degraded grasslands. However, soil microbial community responses to N and P additions are still not well understood, especially multiple levels or/and combined N and P additions in high-altitude grasslands. In this study, the single and interactive effects of N and P additions on the soil microbes were explored. A field experiment with two factors (N 0, 7.5, and 15 g N m−2 year−1; P 0, 3.27, and 6.55 g P m−2 year−1) was conducted by a completely randomized block design in a Tibetan plateau steppe. Total and specific microbial biomass (bacteria, fungi, G+/G− bacteria, saprotrophs, actinomycetes, and arbuscular mycorrhizal fungi) were analyzed by using phospholipid fatty acids (PLFAs). Additionally, based on their fixed weight composites, we used a composite variable (phenotype) to represent the microbial community. The results showed that N addition decreased the microbe phenotype, total microbial biomass, and specific microbial biomass (total bacteria, G+, and G− bacteria). P application and its interaction with N application all increased the microbial phenotype, total microbial biomass, and specific microbial biomass (total bacteria, G+, G−, saprotrophs, and actinomycetes). Besides, the microbial phenotype was positively correlated with P application rates and not correlated with N application rates. In conclusion, P was the key limiting factor for soil microbes, and its interaction with N is also important for some specific microbes. In addition, long-term responses of soil microbes after N and P amendments need further investigation in the Tibetan alpine steppe.

Substitution of manure for chemical fertilizer affects soil microbial community diversity, structure and function in greenhouse vegetable production systems.

Soil microbial communities and enzyme activities together affect various ecosystem functions of soils. Fertilization, an important agricultural management practice, is known to modify soil microbial characteristics; however, inconsistent results have been reported. The aim of this research was to make a comparative study of the effects of different nitrogen (N) fertilizer rates and types (organic and inorganic) on soil physicochemical properties, enzyme activities and microbial attributes in a greenhouse vegetable production (GVP) system of Tianjin, China. Results showed that manure substitution of chemical fertilizer, especially at a higher substitution rate, improved soil physicochemical properties (higher soil organic C (SOC) and nutrient (available N and P) contents; lower bulk densities), promoted microbial growth (higher total phospholipid fatty acids and microbial biomass C contents) and activity (higher soil hydrolase activities). Manure application induced a higher fungi/bacteria ratio due to a lower response in bacterial than fungal growth. Also, manure application greatly increased bacterial stress indices, as well as microbial communities and functional diversity. The principal component analysis showed that the impact of manure on microbial communities and enzyme activities were more significant than those of chemical fertilizer. Furthermore, redundancy analysis indicated that SOC and total N strongly influenced the microbial composition, while SOC and ammonium-N strongly influenced the microbial activity. In conclusion, manure substitution of inorganic fertilizer, especially at a higher substitution rate, was more efficient for improving soil quality and biological functions.

Consistent effects of a non-native earthworm on soil microbial communities in three subtropical forests

Non-native earthworms have increasingly become a global problem due to the strong effects they exert on biodiversity and ecosystem functions in their introduced habitat. Quantifying interactions between non-native earthworm and microbial communities in forest ecosystems should increase our understanding of non-native earthworm-induced changes in soil biogeochemical cycles and plant diversity. In a microcosm experiment, we investigated non-native earthworm-microbial interactions in soils originating from three typical subtropical forests in which pan-tropical non-native Pontoscolex corethrurus (Müller, 1857) was the dominant earthworm. Our study showed that P. corethrurus strongly affected the soil microbial communities in all three soils. The cast production and burrowing activities of P. corethrurus significantly reduced total soil microbial biomass and soil bacterial biomass, but did not change soil fungal biomass. As a consequence, P. corethrurus substantially increased the ratio of fungi to bacteria. For most soil microbial properties, these effects occurred in all three soils, i.e., they were independent of habitat type. Furthermore, the microbial communities in the three forest soils were found to be more similar with than without P. corethrurus. These results suggest that P. corethrurus can greatly affect soil microbial communities in a variety of habitats where the earthworm has been introduced. Our results also showed that microbial biomass was substantially higher in the P. corethrurus gut than in the surrounding soil and that new habitat types can modify the microbial community in the gut of P. corethrurus.

Effects of vegetation type on the microbial characteristics of the fissure soil-plant systems in karst rocky desertification regions of SW China

In karst regions, shallow karst fissure (SKF) soil has proven to be an important plant habitat and soil resource. However, how plants affect the microbial abundance and community composition of SKF soil remains poorly studied. We explored the soil microbial community structure differences in fractured soil-plant systems by determining phospholipid fatty acid (PLFA) profiles under three vegetation types (herbs, shrubs and trees) in SKF and used a bare SKF without vegetation as the control in a karst rocky desertification area. The total microbial biomass and microbial community composition differed between surface soil and SKF soil. The total microbial biomass in surface soil was higher than that in SKF soil. In addition, in contrast to surface soil, the microbial communities in SKF soil were more vulnerable to the effects of environmental variables. Furthermore, plants had a significant positive effect on the accumulation of microbial biomass in surface and SKF soil: shrubs had the strongest effect, followed by trees. Vegetation types significantly affected the ratios of saturated PLFAs to monounsaturated PLFAs (SAT/MONO ratio) and cyclopropyl PLFAs to precursors (cy/pre ratio). In contrast to the SKF without vegetation, the SAT/MONO ratio and cy/pre ratio under grasslands, shrublands and trees were low. Herbs and shrubs had the greatest capacity to enhance the ability of soil to respond to environmental stress compared to trees. Our results suggest that, as an important plant habitat in karst regions, the condition of SKF soil should be urgently improved. The stereoscopic collocation of shrub-grass vegetation may be the preferred measure for vegetation restoration. Deep-rooted shrubs and grasses are best at improving soil and plant growth. Our study can be useful for developing strategies for vegetation rehabilitation in karst regions.

Assessing soil resilience across an agricultural land retirement chronosequence

Reestablishment of perennial vegetation can improve soil conditions on intensively cultivated lands, but the timeframe required to recover uncultivated soil quality is not well understood. This study aimed to measure the recovery of soil physical (bulk density, aggregate stability, and water infiltration rate), biological (total microbial biomass and soil respiration), and chemical (surface soil organic carbon [SOC]) parameters across a 30-year land retirement chronosequence. Soil parameters on lands retired under long- and short-term Conservation Reserve Program (CRP) enrollment periods were compared to undisturbed and actively cropped lands, and chronofunctions were utilized to estimate the time required to achieve uncultivated soil quality. Results showed that short-term enrollment was not sufficient to restore any parameters to uncultivated quality, although bulk density, water infiltration, soil respiration, and total organic carbon (C) levels generally trended toward the undisturbed condition. No significant differences between the uncultivated and 30-year CRP enrollment for aggregate stability and total microbial biomass suggests uncultivated soil quality was restored within 30 years of land retirement. Based on chronofunction analysis, an estimated period of 53 years would be necessary to return bulk density and soil respiration to undisturbed quality on retired land. Water infiltration and SOC had the longest predicted recovery time of 75 and 128 years, respectively. These results suggest soil properties recover at varying rates once retired into perennial grassland systems, and long-term land retirement is necessary to restore soil properties to precultivation condition and maintain high quality soils capable of providing key ecosystem services.

Contrasting Response of Nutrient Acquisition Traits in Wheat Grown on Bisphenol A-Contaminated Soils

Repeated application of organic fertiliser has unintentionally let to the introduction into surface water and soils of many phytotoxic substances that compromise agricultural production and threaten environmental quality. Recent studies using hydroponic systems have reported that bisphenol A (BPA) affects essential mineral elements contents and root absorptive function, thereby impacting nutrient content in plant. However, in soils, plants develop specific traits related to nutrient acquisition strategies. In order to ensure optimised supply of nutrients, understanding the response of these traits under BPA stress is thus essential. Here, we therefore, investigated how leaf nutrient contents (P, Ca and K), root morphology, P-mobilising exudates and rhizospheric microbiota biomass respond to BPA soil contamination using wheat (Triticum aestivum) as plant model. After 7 weeks, root and leaf traits were not markedly affected by the exposure to BPA at low and high concentrations (0.1 and 1000 mg kg−1 soil). Significant change on average root diameter and aerial biomass were only observed at the highest dose. BPA contamination had no influence on nutrients acquisition traits and root-associated microbiota. Specific root length, carboxylates exudation and P, Ca and K concentrations in leafs were similar irrespective of the treatments. In addition, total microbial biomass, bacteria and fungi abundance measured through phospholipid fatty acid analysis did not differ among controls and contaminated soils. In summary, this experiment suggests a limited influence of BPA contaminated soils on traits involved in nutrient acquisition in wheat.

Effect of microbial growth rate on temperature and metabolic water recorded in 18O/16O ratios of PO4 in DNA

It has been recently demonstrated that both temperature and intracellular/metabolic water are recorded by the PO4 moieties comprising the backbone of DNA in microbial cells as well as in total microbial biomass PO4 (Blake et al., 2016; Li et al., 2016). Temperature and intracellular water composition are reflected in the 18O/16O ratio of PO4 (δ18OP) in DNA (Blake et al., 2016). To determine whether the reported temperature recording by microbial DNA-PO4 could be an artifact of variable microbial growth rate, which may also vary as a function of temperature, three strains of microorganisms having distinct and different growth rate patterns between 23 and 42 °C—Pseudomonas fluorescens, Acinetobacter ADP1 and Marinobacter aquaeolei were cultured over a range of temperatures and growth rate patterns. Growth curve patterns for the different strains were distinct and growth rates increased with temperature. However, as we show here, variations in δ18OP values of DNA-PO4 did not correlate with changes in bacterial growth rates at a given temperature, and O isotope fractionations (i.e., partitioning of O isotopes) between PO4 in DNA and O in water were not significantly different between strains (<1‰). Results suggest that for some microbial strains, strain-specific growth rates could cause minor variation in δ18OP values of microbial DNA independent of temperature effects. Thus, we interpret observed trends as strain-specific, intrinsic differences in growth patterns that do not significantly overprint the recording of temperature and intracellular water O isotopic composition by PO4 comprising the backbone of DNA.

Glucose triggers strong taxon-specific responses in microbial growth and activity: insights from DNA and RNA qSIP.

Growth of soil microorganisms is often described as carbon limited, and adding labile carbon to soil often results in a transient and large increase in respiration. In contrast, soil microbial biomass changes little, suggesting that growth and respiration are decoupled in response to a carbon pulse. Alternatively, measuring bulk responses of the entire community (total respiration and biomass) could mask ecologically important variation among taxa in response to the added carbon. Here, we assessed taxon-specific variation in cellular growth (measured as DNA synthesis) and metabolic activity (measured as rRNA synthesis) following glucose addition to soil using quantitative stable isotope probing with H218 O. We found that glucose addition altered rates of DNA and rRNA synthesis, but the effects were strongly taxon specific: glucose stimulated growth and rRNA transcription for some taxa, and suppressed these for others. These contrasting taxon-specific responses could explain the small and transient changes in total soil microbial biomass. Responses to glucose were not well predicted by a priori assignments of taxa into copiotrophic or oligotrophic categories. Across all taxa, rates of DNA and rRNA synthesis changed in parallel, indicating that growth and activity were coupled, and the degree of coupling was unaffected by glucose addition. This pattern argues against the idea that labile carbon addition causes a large reduction in metabolic growth efficiency; rather, the large pulse of respiration observed with labile substrate addition is more likely to be the result of rapid turnover of microbial biomass, possibly due to trophic interactions. Our results support a strong connection between rRNA synthesis and bacterial growth, and indicate that taxon-specific responses among soil bacteria can buffer responses at the scale of the whole community.

Biological controls over the abundances of terrestrial ammonia oxidizers

AbstractAimAmmonia‐oxidizing archaea (AOA) and bacteria (AOB) are the primary agents for nitrification, converting ammonia (NH4+) into nitrate (NO3−) and modulating plant nitrogen (N) utilization and terrestrial N retention. However, there is still lack of a unifying framework describing the patterns of global AOA and AOB distribution. In particular, biotic interactions are rarely integrated into any of the conceptual models.LocationWorld‐wide.Time period2005–2016.Major taxa studiedAmmonia‐oxidizing archaea and ammonia‐oxidizing bacteria.MethodsA meta‐analysis and synthesis were conducted to obtain a general picture of global AOA and AOB distribution and identify the primary driving factors. A microcosm experiment was then conducted to assess effects of relative carbon to nitrogen availability for heterotrophic microbes on AOA and AOB in two distinct soils. A mesocosm experiment was further carried out to characterize the effects of plant roots and their arbuscular mycorrhizal fungi (AMF) on AOA and AOB abundances using hyphae‐ or root‐ingrowth techniques.ResultsOur meta‐analysis showed that soil carbon to nitrogen (C/N) ratios explained the most variance in AOA and AOB abundances, although soil pH had a significant effect. Experimental results demonstrated that high cellulose and mineral N inputs increased total microbial biomass and microbial activities, but inhibited AOA and AOB, suggesting microbial inhibition of AOA and AOB. Also, AMF and roots suppressed AOA and AOB, respectively.Main conclusionsOur study provides convincing evidence illustrating that relative carbon to nitrogen availability can predominantly affect the abundances of AOA and AOB. Our experimental results further validate that biotic competition among plants, heterotrophic microbes and ammonia oxidizers for substrate N is the predominant control upon AOA and AOB abundances. Together, these findings provide new insights into the role of abiotic and biotic factors in modulating terrestrial AOA and AOB abundances and their potential applications for management of nitrification in an increasing reactive N world.

Water availability regulates negative effects of species mixture on soil microbial biomass in boreal forests

Soil microorganisms are critical for the maintenance of terrestrial biodiversity and ecosystem functions. Both plant diversity and water availability are individually known to influence soil microorganisms; however, their interactive effects remain largely unknown. Here, we investigated whether the effects of tree species mixtures on microbial biomass and composition were altered by water availability. This was accomplished by sampling soils in the growing season from stands that were dominated by Populus tremuloides and Pinus banksiana, respectively, and their relatively even mixtures under reduced (−25% throughfall), ambient, and added (+25% throughfall) water. Microbial community biomass and composition were determined by phospholipid fatty acid analysis. We found that water addition increased soil total microbial biomass and by individual groups, whereas water reduction had no effect. Under ambient water conditions, soil total microbial biomass, arbuscular mycorrhizal fungal, bacterial, gram-positive (GP) bacterial, and gram-negative (GN) bacterial biomass were significantly lower in mixtures than from those of constituent monocultures, but saprotrophic fungal biomass and the ratios of fungal/bacterial and GP/GN bacteria were not significantly affected by tree species mixtures. Water reduction increased species mixture effects on total and individual group microbial biomass from negative to neutral, while water addition only increased mixture effects on arbuscular mycorrhizal fungal and GP bacterial biomass. Across all water treatments, soil total and individual group microbial biomass significantly increased with the abundance of broadleaved trees, but only weakly with species richness. Further, microbial community compositions differed significantly with both overstory type and water treatment. Microbial community compositions exhibited strong associations with tree species richness, soil moisture, soil pH, and litterfall production, whereas microbial biomass did not. Our results suggest that higher species diversity is not always of benefit for soil microorganisms; however, mixed tree species have the potential to regulate ecosystem responses to climate change.

Agricultural land use impacts microbial community structure of streambed sediments

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 83:225-236 (2019) - DOI: https://doi.org/10.3354/ame01905 Agricultural land use impacts microbial community structure of streambed sediments Caitlyn A. Griffith1, Peng Shang2, YueHan Lu2, Ethan J. Theuerkauf3, Antonio B. Rodriguez4, Robert H. Findlay1,* 1Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35401, USA 2Department of Geological Sciences, The University of Alabama, 201 7th Ave, Tuscaloosa, Alabama 35485, USA 3Illinois State Geological Survey, Prairie Research Institute, The University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA 4University of North Carolina, Institute of Marine Sciences, 3431 Arendell St, Morehead City, North Carolina 28557, USA *Corresponding author: rfindlay@ua.edu ABSTRACT: Agricultural land use is known to adversely affect freshwater ecosystems, and recent studies have shown that it can significantly alter dissolved organic matter (DOM) concentrations and quality. DOM quantity and quality are key determinants of microbial community structure in streams and have been linked to changes in community abundance and composition. Considering the vital ecological role sediment microbes play in stream ecosystems, it is important to understand how agricultural land use changes affect stream microbial community structure. This study was conducted to determine if variation in sediment microbial biomass community structure could be attributed to differences in agricultural land use. Microbial biomass, microbial community structure, and stream water parameters were compared on 2 dates from 6 sites representing a gradient of agricultural land use from 18 to 64% within the Bear Creek Watershed in northwest Alabama, USA. Total microbial biomass, determined as phospholipid phosphate, was strongly influenced by sediment surface area and, to a lesser extent, correlated with sampling date and land use. Sediment microbial community structure, determined by phospholipid fatty acid analysis, was significantly correlated to percent agricultural land use in the watershed, as well as stream water DOM humification index, and sediment δ15N values and surface area. Microbial community structure also differed between sampling dates. These findings demonstrate that agricultural land use is linked via alteration of stream water and sediment organic matter to changes in sediment microbial structure which may, at least in part, account for widely observed changes in stream ecosystem functioning associated with agricultural activities. KEY WORDS: Microbial community structure · Streams · Agricultural land use · DOM Full text in pdf format Supplementary material PreviousNextCite this article as: Griffith CA, Shang P, Lu Y, Theuerkauf EJ, Rodriguez AB, Findlay RH (2019) Agricultural land use impacts microbial community structure of streambed sediments. Aquat Microb Ecol 83:225-236. https://doi.org/10.3354/ame01905 Export citation Mail this link - Contents Mailing Lists - RSS Facebook - Tweet - linkedIn Cited by Published in AME Vol. 83, No. 3. Online publication date: October 02, 2019 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2019 Inter-Research.

Effect of long‐term mineral fertilisation on soil microbial abundance, community structure and diversity in a Typic Hapludoll under intensive farming systems

AbstractFertiliser application can not only influence plant communities, but also the soil microbial community dynamics, and consequently soil quality. Specifically, mineral fertilisation can directly or indirectly affect soil chemical properties, microbial abundance and, the structure and diversity of soil microbial communities. We investigated the impact of six different mineral fertiliser regimes in a maize/soybean rotation system: control (CK, without fertilisation), PS (application of phosphorus plus sulphur), NS (application of nitrogen plus S), NP (application of N plus P), NPS (application of N, P plus S) and NPSm (application of N, P, S plus micronutrients). Soil samples were collected at the physiological maturity stage of maize and soybean in March of 2013 and 2014, respectively. Overall, mineral fertilisation resulted in significantly decreased soil pH and increased total organic carbon compared with the control (CK). The analysis of terminal restriction fragment length polymorphism (T‐RFLP) revealed that mineral fertilisers caused a shift in the composition of both bacterial and fungal communities. In 2013, the highest value of Shannon diversity of bacterial terminal restriction fragments (TRFs) was found in control soils. In 2014, NPSm treated soils showed the lowest values of diversity for both bacterial and fungal TRFs. In both crop growing seasons, the analysis of phospholipid fatty acid (PLFA) detected the lowest value of total microbial biomass under CK. As PLFA analysis can be used to evaluate total microbial community, this result suggests that fertilisation increased total microbial biomass. When the bacterial and fungal abundance were examined using real time polymerase chain reaction, the results revealed that mineral fertilisation led to decreased bacterial abundance (16S rRNA), while fungal abundance (18S rRNA) was found to be increased in both crop growing seasons. Our results show that mineral fertiliser application has a significant impact on soil properties, bacterial and fungal abundance and microbial diversity. However, further studies are needed to better understand the mechanisms involved in the changes to microbial communities as a consequence of mineral fertilisation.