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Both microbes and plants contribute to soil organic carbon (SOC) formation and retention, but their roles in controlling SOC dynamics in forest soils under Moso bamboo (Phyllostachys edulis) expansion remain unclear. Here, amino sugars and lignin monomers were measured to represent microbial necromass and plant‐derived components, respectively. The observed decline in both amino sugars and lignin monomers during Moso bamboo expansion indicates a reduction in microbial necromass and recalcitrant plant contributions to SOC composition. This could be attributed to a limitation of microbial substrates and proliferation caused by the reduced litter inputs resulting from the expansion. The proportion of microbial necromass contributing to the SOC pool increased, but that of lignin monomers decreased, as SOC content decreased with Moso bamboo expansion. This suggests that the decrease of SOC during bamboo expansion was mainly due to the reduction of lignin, while the increased contribution of microbial‐derived carbon to SOC may serve to improve SOC stability. Our study sheds light on the altered SOC source inputs resulting from Moso bamboo expansion and emphasizes the need for sustainable forestry management practices that differentiate between microbial‐ and plant‐derived carbon pools. [ABSTRACT FROM AUTHOR]

Purpose: The fixation of atmospheric CO2 and N2 by soil bacteria is important to the terrestrial carbon and nitrogen cycles and can be greatly affected by anthropogenic disturbance. The application of mineral fertilizer combined with manure (MCM) has been used to maintain soil quality and improve soil C storage. However, the impacts of MCM on soil CO2-fixing bacteria (CFB) and N2-fixing bacteria (NFB), encoded separately by the cbbL and nifH genes, remain largely unknown. Methods: In this study, we examined how the community structure of soil CFB and NFB from a chronosequence of Moso bamboo forests (6, 10, 15, and 20 years of intensive management) responded to long-term intensive management with MCM and identified the critical determinants that regulated them. Quantitative PCR and high-throughput pyrosequencing of the cbbL and nifH genes were used to analyze the abundance and community composition of CFB and NFB, respectively. Results: Employing MCM enhanced the content of SOC and soil available N, K, although some fluctuating values were observed over the 20-year period. The abundance of cbbL gene decreased significantly (P < 0.05) after 6 years of management and then recovered after 20 years of management. However, the abundance of nifH gene consistently declined over 20 years of management. The diversity of CFB increased significantly after 6 years of management, while that of NFB decreased significantly after 15 years of management compared to the no-fertilizer control. The phylum Proteobacteria was predominant in the CFB and NFB communities. Furthermore, the sum abundance of keystone taxa Rhodopseudomonas, Aminobacter, and Rubrivivax for CFB increased after 20 years of management, while the keystone taxon Bradyrhizobium for NFB decreased after 20 years of management compared to no-fertilizer control. Conclusions: In conclusion, the application of MCM favors the abundance, diversity, and keystone taxa of soil CFB rather NFB, which may improve soil C fixation. [ABSTRACT FROM AUTHOR]

A number of studies have shown an association between soybean (Glycine max (L.) Merr.) seed yield and plant N accumulation, suggesting that yield could be increased by nodulation by superior strains of Bradyrhizobium japonicum. Attempts to evaluate the response of field-grown soybean to bradyrhizobia-mediated increases in N accumulation have been hindered by an inability of introduced strains to compete successfully with indigenous strains. Therefore, to determine the effect of increased N2 fixation on soybean growth and seed yield, an experiment was conducted using soybean seedlings that were nodulated under greenhouse conditions and then transplanted to the field. Two inoculation treatments, USDA 122 and a mixture of bradyrhizobia indigenous to the field site (control), were applied to the seed and seedlings were developed for 21 d in the greenhouse. Prenodulated seedlings were then transplanted to 1.8 m squared field microplots on a Matapeake silt loam (fine-loamy, mixed, mesic Typic Hapludult) with a most probable number of indigenous bradyrhizobial population of 6.1 X 10 to the eighth power cells kg to the -1 soil. Relative to the control, nodulation by USDA 122 increased both N(sub 2) fixed and total shoot N by a 2-yr average of 29%. Plants nodulated by USDA 122 also assimilated more soil N. The increase in N(sub 2) fixation and total N accumulation occurred prior to, but not during, seedfill. The USDA 122 treatment increased seed yield by an average of 31% (90 g m to the -2). The yield increase was associated with increases in pod number, seedfill rate, remobilized dry matter, remobilized N, and vegetative biomass.

The internally transcribed spacer (ITS) sequences of several different members within each of the soybean bradyrhizobial serogroups where available are determined. The analysis has provided evidence that extant bradyrhizobial genomes are the result of reticulate evolutionary events.

• Bamboo invasion consistently increased soil pH and organic C content across three sites. • Bamboo invasion consistently decreased fungal ITS gene abundances across the sites. • Bamboo invasion improved the closeness of soil bacterial but not fungal communities. • Total soil enzyme activities positively correlated with the abundances of fungi rather than bacteria. Moso bamboo (Phyllostachys edulis) invasions into adjacent forests have been reported to threaten aboveground biodiversity and alter belowground soil processes. However, the impacts of bamboo invasion on soil microbial community composition, co-occurrence network and enzyme activity remain largely unknown. We presented a cross site field investigation on soil bacterial and fungal communities and enzyme activities in three forests (an original broadleaf forest, a mixed bamboo-broadleaf forest and a pure bamboo forest) at three sites in South China. Our results showed that bamboo invasion consistently increased soil pH (by 6.72% − 17.56%) and soil organic carbon concentrations (by 11.75% − 40.63%) across the three sites. Bamboo invasion consistently decreased fungal ITS gene abundances across the sites, but had little effect on bacterial 16S rRNA gene abundances and diversity indices. The community composition of both bacteria and fungi and their functional guilds differed among the three sites and were significantly (P < 0.05) affected by bamboo invasion. Bamboo invasion significantly decreased the relative abundances of ectomycorrhizal but increased those of soil saprotrophs. The complexity of co-occurrence network of bacterial communities was increased whereas that of fungal communities was decreased due to bamboo invasion. The activities of soil enzymes involved in C, N and P cycling were also altered by bamboo invasion, and they were significantly positively correlated with the abundances of fungal ITS gene and ectomycorrhizal rather than those of bacteria and predicted metabolic function. This study suggested that bamboo invasions into adjacent broadleaf forests had contrasting effects on soil bacterial and fungal communities by shifting microhabitats towards a condition that is unfavorable for some fungal functional guilds, which were tightly associated with soil functioning. These results highlight the need for sustainable forestry management against bamboo invasion to maintain fungal diversity and network complexity. [ABSTRACT FROM AUTHOR]

The limited host range of Enterococcus faecalis may reduce its clonal diversity and thereby increase its geographic sharing of ribotype patterns. Such sharing would be advantageous for bacterial source tracking (BST). We determined the geographic sharing of ribotype patterns in 752 Ent. faecalis isolates obtained primarily from wastewater treatment plants in Delaware (15 locations; 490 isolates), Georgia (2 locations; 48 isolates), Idaho (1 location; 118 isolates), New York (2 locations; 48 isolates), and Puerto Rico (2 locations; 48 isolates). Isolates were ribotyped with a RiboPrinter. When pooled across all locations and analyzed at a similarity index of 100% and a tolerance level of 1.00%, the 752 Ent. faecalis isolates yielded 652 different ribotypes, of which 429 (66%) were unshared. Even when the matching criterion was relaxed by decreasing the tolerance level from 1% to 10% or lowering the similarity cutoff from 100% to 90%, half or almost half of the ribotypes were unshared. A Mantel test of zero correlation showed no statistically significant correlation between ribotype patterns and geographic distance among the 32 samples (one location at one time) at either the 1.00% (P = 0.91) or 10.00% (P = 0.83) tolerance levels. Therefore, the percentage of ribotype patterns shared between two locations did not increase as the distance between locations decreased. In the case of BST, a permanent host origin database sufficiently large to encompass these ribotype patterns would be time-consuming and expensive to construct. [ABSTRACT FROM AUTHOR]

Two studies were conducted to evaluate microbial populations in polycyclic aromatic hydrocarboncontaminated soil. Captina silt loam was freshly exposed to (1) 0 or 2000 mg pyrene/kg and sampled after 10- and 61-wk incubation and (2) 0 or 505 mg pyrene + 445 mg phenanthrene/kg and sampled after a 21-wk incubation. Microbial numbers were determined by plate-count techniques. Isolated bacteria, selected degraders, and wholesoil extracts were analyzed by fatty acid methyl ester analysis (FAME). In the pyrene experiment, pyrene did not affect total bacterial or fungal numbers, but pyrene degraders increased from undetectable levels to 7.09 log 10 degraders/g in the contaminated soil. The FAME analysis of bacterial isolates detected no pyrene effect, but wholesoil FAME indicated an increase in the contaminated soil of a fatty acid characteristic of protozoa and a major fatty acid detected in isolated degraders. In the pyrene + phenanthrene experiment, the contaminants had no impact on bacterial, fungal, or actinomycete numbers but increased degrader numbers. No effect of pyrene + phenanthrene was detected by isolate FAME, but whole-soil FAME indicated an effect similar to that in the pyrene experiment. The results indicate that pyrene, although not impacting microbial numbers, may have altered the soil microbial composition and that Captina silt loam can develop an effective degrader population under tested conditions. [ABSTRACT FROM AUTHOR]

Coal fly ash may be a valuable soil amendment because it contains plant nutrients and liming agents and has a silty texture that can improve the water-holding capacities of sandy, drought-prone soils. Short-term laboratory studies have indicated that addition of unweathered fly ash to soil can stress microbial populations and their activities, but effects of fly ash addition at the field scale are not known. In this study, field plots received 0 or 505 Mg fly ash ha- 1 (incorporated by conventional tillage to a depth of 40 cm) and were subsequently cropped to a fallow-com (Zea mays L.)-wheat (Triticum aestivum L.) rotation or continuous fescue (Festuca arundinacea Schreb.). Twenty months later, during the wheat phase of the rotation, theplots were sampled (0--15 cm) and assayed for activity of soil enzymes (dehydrogenase, alkaline phosphatase, arylsulfatase, and denitrifying enzymes); numbers of aerobic heterotrophs, ammonium oxidizers, denitrifiers, and bradyrhizobia. and N mineralization, nitrification, and denitrification potentials. Nitrification potentials doubled in fly ash-amended soils, and numbers of denitrifiers were 200-fold higherin fescue-cropped, fly ash-amended soils relative to fescue-cropped,nonamended soils. No other large differences in microbial populations or activities were found. The lack of detrimental effects on microorganisms in the field was possibly due to reductions in fly ash's soluble salt and trace element concentrations with time, the mild alkalinity of the fly ash used in this study, and the positive responses ofcrops to fly ash amendment. [ABSTRACT FROM AUTHOR]

Abstract: Water soluble anionic polyacrylamide (PAM) is a highly effective erosion preventing and infiltration enhancing polymer, when applied at rates of 1–10gm−3 in furrow irrigation water. PAM greatly reduces sediment, nutrients, pesticides and coliform bacteria in irrigation runoff. There has been some concern about the potential for PAM accumulation to affect microbial ecology. We ran a long-term study applying massive quantities of PAM to soil and monitored its impact on soil microbial potential. In June, July and August, we measured active soil bacterial and fungal biomass and microbial diversity in soils receiving 0 (control), 2691 and 5382kg active ingredient (ai) PAMha−1. Active bacterial biomass in soil was 20–30% greater in the control treatment than in soil treated with 2691 or 5382kg ai PAMha−1 in June and August, but not July. Active fungal biomass in soils was 30–50% greater in the control treatment than soil treated with 2691 or 5382kg ai PAMha−1 in June and July, but not August. Active microbial biomass in soil was 27–48% greater in the untreated control than soil treated with 2691 or 5382kg ai PAMha−1 except in June. Whole soil fatty acid profiles showed no discernible change in the soil microbial community due to either of the PAM treatments at any sampling time. Analysis of nutritional characteristics using Biolog GN plates, however, yielded an apparent separation of the non-amended control soils from those plots receiving the high PAM application rate in June, but not in July or August. In contrast, comparisons of the three sampling times by both the fatty acid and Biolog analyses indicated that the microbial metabolic potential present in June were different from those sampled in July and August. Although PAM application to soil or irrigation water in some cases may reduce active bacterial and fungal biomass it does not seem to appreciably affect the soil microbial metabolic potential. [Copyright &y& Elsevier]

Biochar incorporated into soil has been known to affect soil nutrient availability and act as a habitat for microorganisms, both of which could be related to its particle size. However, little is known about the effect of particle size on soil microbial community structure and function. To investigate short-term soil microbial responses to biochar addition having varying particle sizes and addition rates, we established a laboratory incubation study. Biochar produced via pyrolysis of bamboo was ground into three particle sizes (diameter size < 0.05 mm (fine), 0.05–1.0 mm (medium) and 1.0–2.0 mm (coarse)) and amended at rates of 0% (control), 3% and 9% (w/w) in an intensively managed bamboo ( Phyllostachys praecox ) plantation soil. The results showed that the fine particle biochar resulted in significantly higher soil pH, electrical conductivity (EC), available potassium (K) concentrations than the medium and coarse particle sizes. The fine-sized biochar also induced significantly higher total microbial phospholipid fatty acids (PLFAs) concentrations by 60.28% and 88.94% than the medium and coarse particles regardless of addition rate, respectively. Redundancy analysis suggested that the microbial community structures were largely dependent of particle size, and that improved soil properties were key factors shaping them. The cumulative CO 2 emissions from biochar-amended soils were 2–56% lower than the control and sharply decreased with increasing addition rates and particle sizes. Activities of α-glucosidase, β-glucosidase, β-xylosidase, N -acetyl-β-glucosaminidase, peroxidase and dehydrogenase decreased by ranging from 7% to 47% in biochar-amended soils over the control, indicating that biochar addition reduced enzyme activities involved carbon cycling capacity. Our results suggest that biochar addition can affect microbial population abundances, community structure and enzyme activities, that these effects are particle size and rate dependent. The fine particle biochar may additionally produce a better habitat for microorganisms compared to the other particle sizes. [ABSTRACT FROM AUTHOR]

Viruses are the most abundant and diverse biological entities within soils, yet their ecological impact is largely unknown. Defining how soil viral communities change with perturbation or across environments will contribute to understanding the larger ecological significance of soil viruses. A new approach to examining the composition of soil viral communities based on random PCR amplification of polymorphic DNA (RAPD-PCR) was developed. A key methodological improvement was the use of viral metagenomic sequence data for the design of RAPD-PCR primers. This metagenomically informed approach to primer design enabled the optimization of RAPD-PCR sensitivity for examining changes in soil viral communities. Initial application of RAPD-PCR viral fingerprinting to soil viral communities demonstrated that the composition of autochthonous soil viral assemblages noticeably changed over a distance of meters along a transect of Antarctic soils and across soils subjected to different land uses. For Antarctic soils, viral assemblages segregated upslope from the edge of dry valley lakes. In the case of temperate soils at the Kellogg Biological Station, viral communities clustered according to land use treatment. In both environments, soil viral communities changed along with environmental factors known to shape the composition of bacterial host communities. Overall, this work demonstrates that RAPD-PCR fingerprinting is an inexpensive, high-throughput means for addressing first-order questions of viral community dynamics within environmental samples and thus fills a methodological gap between narrow single-gene approaches and comprehensive shotgun metagenomic sequencing for the analysis of viral community diversity. [ABSTRACT FROM AUTHOR]

Water is a crucial factor controlling the fate and processing of soil organics. Water commonly flows through the vadose zone via preferential flow pathways, resulting in nonuniform and rapid infiltration. Hence, a large portion of the soil matrix is bypassed. Preferential flow paths, often associated with well-connected macropore networks (>300 μm Ø), offer a unique balance between water availability, nutrient delivery, and re-oxygenation upon drainage. The heightened concentrations of moisture, nutrients, and oxygen make these locations optimal for high rates of microbial activity. Flow paths often display temporal stability. This stability results in repeated wetting and biogeochemical reactivation through time creating a lasting impact on micro-environmental conditions relevant to microbial functioning and carbon cycling in soil. Despite decades of research on preferential flow, there is still a need to link flow paths and the resultant heterogeneous moisture distributions to soil function. In this review, we discuss how preferential flow can serve as a framework of reference for the spatially and temporally heterogeneous biogeochemical cycling of soil carbon. We highlight the importance of combining current knowledge of pore-scale carbon dynamics with an appreciation of connected networks of hydraulically active pores/paths within the soil profile. Such combination opens new possibilities for upscaling pore-scale processes with the inclusion of resource heterogeneity at the macroscale. Working within this hydraulically connected framework can provide insight for the mechanistic representation of hot moments, which are temporally isolated large pulses of CO 2 after rewetting or thawing events. We conclude with suggestions on knowledge gaps and stress the critical need of linking soil physics with biology to mechanistically understand soil functions. • Preferential flow paths play a key role in soil carbon dynamics. • Pore-scale carbon dynamics could be upscaled using hydraulic connectivity. • A conceptual model is presented that considers how soil pores function from hydrological and microbial perspective. [ABSTRACT FROM AUTHOR]

The ability of Bradyrhizobium spp. to nodulate and fix atmospheric nitrogen in soybean root nodules is critical to meeting humanity's nutritional needs. The intricacies of soybean bradyrhizobia-plant interactions have been studied extensively; however, bradyrhizobial ecology as influenced by phages has received somewhat less attention, even though these interactions may significantly impact soybean yield. In batch culture, four soybean bradyrhizobia strains, Bradyrhizobium japonicum S06B (S06B-Bj), B. japonicum S10J (S10J-Bj), Bradyrhizobium diazoefficiens USDA 122 (USDA 122-Bd), and Bradyrhizobium elkanii USDA 76 T (USDA 76-Be), spontaneously (without apparent exogenous chemical or physical induction) produced tailed phages throughout the growth cycle; for three strains, phage concentrations exceeded cell numbers by ~3-fold after 48 h of incubation. Phage terminase large-subunit protein phylogeny revealed possible differences in phage packaging and replication mechanisms. Bioinformatic analyses predicted multiple prophage regions within each soybean bradyrhizobia genome, preventing accurate identification of spontaneously produced prophage (SPP) genomes. A DNA sequencing and mapping approach accurately delineated the boundaries of four SPP genomes within three of the soybean bradyrhizobia chromosomes and suggested that the SPPs were capable of transduction. In addition to the phages, S06B-Bj and USDA 76-Be contained three to four times more insertion sequences (IS) and large, conjugable, broad host range plasmids, both of which are known drivers of horizontal gene transfer (HGT) in soybean bradyrhizobia. These factors indicate that SPP along with IS and plasmids participate in HGT, drive bradyrhizobia evolution, and play an outsized role in bradyrhizobia ecology. IMPORTANCE Previous studies have shown that IS and plasmids mediate HGT of symbiotic nodulation ( nod ) genes in soybean bradyrhizobia; however, these events require close cell-to-cell contact, which could be limited in soil environments. Bacteriophage-assisted gene transduction through spontaneously produced prophages provides a stable means of HGT not limited by the constraints of proximal cell-to-cell contact. These phage-mediated HGT events may shape soybean bradyrhizobia population ecology, with concomitant impacts on soybean agriculture.

Microbial source tracking (MST) results, obtained using identical sample sets and pulsed field gel electrophoresis (PFGE), repetitive element PCR (rep-PCR) and ribotyping techniques were compared. These methods were performed by six investigators in analysis of duplicate, blind sets of water samples spiked with feces from five possible sources (sewage, human, dog, cow and seagull). Investigators were provided with samples of the fecal material used to inoculate the water samples for host origin database construction. All methods correctly identified the dominant source in the majority of the samples. Modifications of some of these methods correctly identified the dominant sources in over 90% of the samples; however, false positive rates were as high as 57%. The high false positive rates appeared to be indirectly proportional to the levels of stringency applied in pattern analysis. All the methods produced useful data but the results highlighted the need to modify and optimize these methods in order to minimize sources of error.