Nitric oxide reductase-targeted real-time PCR quantification of denitrifier populations in soil

The quantification of denitrifying bacteria is a component in the further understanding of denitrification processes in the environment. Real-time PCR primers were designed to target two segments of the denitrifier population (cnorB(P) [Pseudomonas mandelii and closely related strains] and cnorB(B) [Bosea, Bradyrhizobium, and Ensifer spp.]) in agricultural soils based on functional cnorB (nitric oxide reductase) gene sequences. Total population numbers were measured using 16S rRNA gene real-time PCR. Two soil microcosm experiments were conducted. Experiment 1 examined the response of the indigenous soil microbial population to the addition of 500 mg/kg glucose-C daily over 7 days in soil microcosms. Changes in the total population were correlated (r = 0.83) between 16S rRNA gene copy numbers and microbial biomass carbon estimates. Members of the cnorB(P) population of denitrifiers showed typical r-strategy by being able to increase their proportion in the total population from starting levels of <0.1% to around 2.4% after a daily addition of 500 mg/kg glucose-C. The cnorB(B) guild was not able to increase its relative percentage of the total population in response to the addition of glucose-C, instead increasing copy numbers only in proportion with the total population measured by 16S rRNA genes. Experiment 2 measured population dynamics in soil after the addition of various amounts of glucose-C (0 to 500 mg/kg) and incubation under denitrifying conditions. cnorB(P) populations increased proportionally with the amount of glucose-C added (from 0 to 500 mg/kg). In soil microcosms, denitrification rates, respiration, and cnorB(P) population densities increased significantly with increasing rates of glucose addition. cnorB(B) guild densities did not increase significantly under denitrifying conditions in response to increasing C additions.     

Effect of nitrate and glucose addition on denitrification and nitric oxide reductase (<Emphasis Type="Italic">cnorB</Emphasis>) gene abundance and mRNA levels in <Emphasis Type="Italic">Pseudomonas mandelii</Emphasis> inoculated into anoxic soil

The effect of glucose addition (0 and 500 μg C g⁻¹ soil) and nitrate (NO₃) addition (0, 10, 50 and 500 μg NO₃–N g⁻¹ soil) on nitric oxide reductase (cnorB) gene abundance and mRNA levels, and cumulative denitrification were quantified over 48 h in anoxic soils inoculated with Pseudomonas mandelii. Addition of glucose-C significantly increased cnorB _p (P. mandelii and related species) mRNA levels and abundance compared with soil with no glucose added, averaged over time and NO₃ addition treatments. Without glucose addition, cnorB _p mRNA levels were higher when 500 μg NO₃–N g⁻¹ soil was added compared with other NO₃ additions. In treatments with glucose added, addition of 50 μg NO₃–N g⁻¹ soil resulted in higher cnorB _p mRNA levels than soil without NO₃ but was not different from the 10 and 500 μg NO₃–N g⁻¹ treatments. cnorB _p abundance in soils without glucose addition was significantly higher in soils with 500 μg NO₃–N g⁻¹ soil compared to lower N-treated soils. Conversely, addition of 500 μg NO₃–N g⁻¹ soil resulted in lower cnorB _p abundance compared with soil without N-addition. Over 48 h, cumulative denitrification in soils with 500 μg glucose-C g⁻¹ soil, and 50 or 500 μg NO₃–N g⁻¹ was higher than all other treatments. There was a positive correlation between cnorB _p abundance and cumulative denitrification, but only in soils without glucose addition. Glucose-treated soils generally had higher cnorB _p abundance and mRNA levels than soils without glucose added, however response of cnorB _p abundance and mRNA levels to NO₃ supply depended on carbon availability.     

Nutrient Amendments in Soil DNA Stable Isotope Probing Experiments Reduce the Observed Methanotroph Diversity

Stable isotope probing (SIP) can be used to analyze the active bacterial populations involved in a process by incorporating ¹³C-labeled substrate into cellular components such as DNA. Relatively long incubation times are often used with laboratory microcosms in order to incorporate sufficient ¹³C into the DNA of the target organisms. Addition of nutrients can be used to accelerate the processes. However, unnatural concentrations of nutrients may artificially change bacterial diversity and activity. In this study, methanotroph activity and diversity in soil was examined during the consumption of ¹³CH₄ with three DNA-SIP experiments, using microcosms with natural field soil water conditions, the addition of water, and the addition of mineral salts solution. Methanotroph population diversity was studied by targeting 16S rRNA and pmoA genes. Clone library analyses, denaturing gradient gel electrophoresis fingerprinting, and pmoA microarray hybridization analyses were carried out. Most methanotroph diversity (type I and type II methanotrophs) was observed in nonamended SIP microcosms. Although this treatment probably best reflected the in situ environmental conditions, one major disadvantage of this incubation was that the incorporation of ¹³CH₄ was slow and some cross-feeding of ¹³C occurred, thereby leading to labeling of nonmethanotroph microorganisms. Conversely, microcosms supplemented with mineral salts medium exhibited rapid consumption of ¹³CH₄, resulting in the labeling of a less diverse population of only type I methanotrophs. DNA-SIP incubations using water-amended microcosms yielded faster incorporation of ¹³C into active methanotrophs while avoiding the cross-feeding of ¹³C.     

Methyl t-Butyl Ether Mineralization in Surface-Water Sediment Microcosms under Denitrifying Conditions

Mineralization of [U-¹⁴C]methyl t-butyl ether (MTBE) to ¹⁴CO₂ without accumulation of t-butyl alcohol (TBA) was observed in surface-water sediment microcosms under denitrifying conditions. Methanogenic activity and limited transformation of MTBE to TBA were observed in the absence of denitrification. Results indicate that bed sediment microorganisms can effectively degrade MTBE to nontoxic products under denitrifying conditions.     

Microbial Populations Responsive to Denitrification-Inducing Conditions in Rice Paddy Soil,as Revealed by Comparative 16S rRNA Gene Analysis

Rice paddy soil has been shown to have strong denitrifying activity. However, the microbial populations responsible for nitrate respiration and denitrification have not been well characterized. In this study, we performed a clone library analysis of >1,000 clones of the nearly full-length 16S rRNA gene to characterize bacterial community structure in rice paddy soil. We also identified potential key players in nitrate respiration and denitrification by comparing the community structures of soils with strong denitrifying activity to those of soils without denitrifying activity. Clone library analysis showed that bacteria belonging to the phylum Firmicutes, including a unique Symbiobacterium clade, dominated the clones obtained in this study. Using the template match method, several operational taxonomic units (OTUs), most belonging to the orders Burkholderiales and Rhodocyclales, were identified as OTUs that were specifically enriched in the sample with strong denitrifying activity. Almost one-half of these OTUs were classified in the genus Herbaspirillum and appeared >10-fold more frequently in the soils with strong denitrifying activity than in the soils without denitrifying activity. Therefore, OTUs related to Herbaspirillum are potential key players in nitrate respiration and denitrification under the conditions used.Rice is one of the most important agronomic plants in the world (20). More than 135 million ha are used for rice cultivation worldwide, 88% of which consists of paddy fields (i.e., flooded fields) (16). Since rice paddy soil has limited available oxygen, various anaerobic biochemical processes can occur, including methane production, Mn⁴⁺ and Fe³⁺ reduction, nitrate respiration, and denitrification.Denitrification is a microbial respiratory process during which soluble nitrogen oxides (NO₃⁻ and NO₂⁻) are reduced to gaseous products (NO, N₂O, and N₂) (14, 43). Reduction of nitrate (NO₃⁻) to nitrite (NO₂⁻) is part of the denitrification process; however, this reaction can also be performed by nondenitrifiers. Reduction of nitrate to nitrite as an end product is called nitrate respiration (43). The emission of N₂O from rice paddy soils is less than that from upland crop fields (2), which is probably due to complete nitrate-nitrite reduction to N₂, since rice paddy soil is known to have strong denitrifying activity (28). However, the microbes responsible for denitrification in rice paddy soil are not well known.Denitrifying ability is sporadically distributed among taxonomically diverse groups of bacteria, as well as some archaea and fungi (14, 33, 43). Therefore, it is difficult to identify denitrifying organisms based only on their 16S rRNA gene sequences (33). However, culture-independent 16S rRNA gene analysis can be used to identify microbial populations responsive to denitrification-inducing conditions if they are properly differentiated from background populations. The 16S rRNA gene can provide taxonomic information about organisms which cannot be obtained from analyses targeting nitrite reductase genes (nirS and nirK) alone (34).One approach to differentiate functionally active populations from background populations is to use stable-isotope probing (SIP) (35). SIP was previously used to identify succinate-assimilating bacterial populations under denitrifying conditions in rice paddy soil, using nitrate and succinate as the electron acceptor and donor, respectively (37). Although SIP analysis can provide solid evidence that links function with taxonomy, it requires assimilation of isotopically labeled substrates. This may limit the application of SIP in studies of dissimilatory processes, such as nitrate respiration and denitrification. For example, previous SIP studies targeted bacteria assimilating ¹³C-labeled acetate, methanol, or succinate under denitrifying conditions (13, 30, 37).Another approach is to detect specifically enriched microbial populations under certain conditions by comparative analysis of 16S rRNA gene sequences (9). This approach does not necessarily require addition of isotopically labeled substrates and therefore has the potential to identify microbes performing dissimilatory processes. Furthermore, the community structure of the total population can also be elucidated in this manner (10, 25, 36). However, the usefulness of comparative analysis of 16S rRNA gene sequences has not been thoroughly tested. In addition, this approach has not been used to study nitrate respirators and denitrifiers.Consequently, the objectives of this study were (i) to characterize the soil bacterial population in rice paddy soil by clone library analysis of >1,000 clones of the nearly full-length 16S rRNA gene and (ii) to identify active bacterial populations under denitrification-inducing conditions by comparing clone libraries.     

Effects of Nitrogen Addition on Litter Decomposition and CO2 Release: Considering Changes in Litter Quantity

This study aims to evaluate the impacts of changes in litter quantity under simulated N deposition on litter decomposition, CO₂ release, and soil C loss potential in a larch plantation in Northeast China. We conducted a laboratory incubation experiment using soil and litter collected from control and N addition (100 kg ha⁻¹ year⁻¹ for 10 years) plots. Different quantities of litter (0, 1, 2 and 4 g) were placed on 150 g soils collected from the same plots and incubated in microcosms for 270 days. We found that increased litter input strongly stimulated litter decomposition rate and CO₂ release in both control and N fertilization microcosms, though reduced soil microbial biomass C (MBC) and dissolved inorganic N (DIN) concentration. Carbon input (C loss from litter decomposition) and carbon output (the cumulative C loss due to respiration) elevated with increasing litter input in both control and N fertilization microcosms. However, soil C loss potentials (C output–C input) reduced by 62% in control microcosms and 111% in N fertilization microcosms when litter addition increased from 1 g to 4 g, respectively. Our results indicated that increased litter input had a potential to suppress soil organic C loss especially for N addition plots.     

Microcosm Enrichment of Biphenyl-Degrading Microbial Communities from Soils and Sediments

A microcosm enrichment approach was employed to isolate bacteria which are representative of long-term biphenyl-adapted microbial communities. Growth of microorganisms was stimulated by incubating soil and sediment samples from polluted and nonpolluted sites with biphenyl crystals. After 6 months, stable population densities between 8 × 10⁹ and 2 × 10¹¹ CFU/ml were established in the microcosms, and a large percentage of the organisms were able to grow on biphenyl-containing minimal medium plates. A total of 177 biphenyl-degrading strains were subsequently isolated and characterized by their ability to grow on biphenyl in liquid culture and to accumulate a yellow meta cleavage product when they were sprayed with dihydroxybiphenyl. Isolates were identified by using a polyphasic approach, including fatty acid methyl ester (FAME) analysis, 16S rRNA gene sequence comparison, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell proteins, and genomic fingerprinting based on sequence variability in the 16S-23S ribosomal DNA intergenic spacer region. In all of the microcosms, isolates identified as Rhodococcus opacus dominated the cultivable microbial community, comprising a cluster of 137 isolates with very similar FAME profiles (Euclidean distances, <10) and identical 16S rRNA gene sequences. The R. opacus isolates from the different microcosms studied could not be distinguished from each other by any of the fingerprint methods used. In addition, three other FAME clusters were found in one or two of the microcosms analyzed; these clusters could be assigned to Alcaligenes sp., Terrabacter sp., and Bacillus thuringiensis on the basis of their FAME profiles and/or comparisons of the 16S rRNA gene sequences of representatives. Thus, the microcosm enrichments were strongly dominated by gram-positive bacteria, especially the species R. opacus, independent of the pollution history of the original sample. R. opacus, therefore, is a promising candidate for development of effective long-term inocula for polychlorinated biphenyl bioremediation.     

Use of Stable-Isotope Probing, Full-Cycle rRNA Analysis, and Fluorescence In Situ Hybridization-Microautoradiography To Study a Methanol-Fed Denitrifying Microbial Community

A denitrifying microbial consortium was enriched in an anoxically operated, methanol-fed sequencing batch reactor (SBR) fed with a mineral salts medium containing methanol as the sole carbon source and nitrate as the electron acceptor. The SBR was inoculated with sludge from a biological nutrient removal activated sludge plant exhibiting good denitrification. The SBR denitrification rate improved from less than 0.02 mg of NO₃⁻-N mg of mixed-liquor volatile suspended solids (MLVSS)⁻¹ h⁻¹ to a steady-state value of 0.06 mg of NO₃⁻-N mg of MLVSS⁻¹ h⁻¹ over a 7-month operational period. At this time, the enriched microbial community was subjected to stable-isotope probing (SIP) with [¹³C]methanol to biomark the DNA of the denitrifiers. The extracted [¹³C]DNA and [¹²C]DNA from the SIP experiment were separately subjected to full-cycle rRNA analysis. The dominant 16S rRNA gene phylotype (group A clones) in the [¹³C]DNA clone library was closely related to those of the obligate methylotrophs Methylobacillus and Methylophilus in the order Methylophilales of the Betaproteobacteria (96 to 97% sequence identities), while the most abundant clone groups in the [¹²C]DNA clone library mostly belonged to the family Saprospiraceae in the Bacteroidetes phylum. Oligonucleotide probes for use in fluorescence in situ hybridization (FISH) were designed to specifically target the group A clones and Methylophilales (probes DEN67 and MET1216, respectively) and the Saprospiraceae clones (probe SAP553). Application of these probes to the SBR biomass over the enrichment period demonstrated a strong correlation between the level of SBR denitrification and relative abundance of DEN67-targeted bacteria in the SBR community. By contrast, there was no correlation between the denitrification rate and the relative abundances of the well-known denitrifying genera Hyphomicrobium and Paracoccus or the Saprospiraceae clones visualized by FISH in the SBR biomass. FISH combined with microautoradiography independently confirmed that the DEN67-targeted cells were the dominant bacterial group capable of anoxic [¹⁴C]methanol uptake in the enriched biomass. The well-known denitrification lag period in the methanol-fed SBR was shown to coincide with a lag phase in growth of the DEN67-targeted denitrifying population. We conclude that Methylophilales bacteria are the dominant denitrifiers in our SBR system and likely are important denitrifiers in full-scale methanol-fed denitrifying sludges.     

Added dietary cobalt or vitamin B12, or injecting vitamin B12 does not improve performance or indicators of ketosis in pre- and post-partum Holstein-Friesian dairy cows

Vitamin B₁₂ is synthesised in the rumen from cobalt (Co) and has a major role in metabolism in the peri-paturient period, although few studies have evaluated the effect of the dietary inclusion of Co, vitamin B₁₂ or injecting vitamin B₁₂ on the metabolism, health and performance of high yielding dairy cows. A total of 56 Holstein-Friesian dairy cows received one of four treatments from 8 weeks before calving to 8 weeks post-calving: C, no added Co; DC, additional 0.2 mg Co/kg dry matter (DM); DB, additional 0.68 mg vitamin B₁₂/kg DM; IB, intra-muscular injection of vitamin B₁₂ to supply 0.71 mg/cow per day prepartum and 1.42 mg/cow per day post-partum. The basal and lactation rations both contained 0.21 mg Co/kg DM. Cows were weighed and condition scored at drying off, 4 weeks before calving, within 24 h of calving and at 2, 4 and 8 weeks post-calving, with blood samples collected at drying off, 2 weeks pre-calving, calving and 2, 4 and 8 weeks post-calving. Liver biopsy samples were collected from all animals at drying off and 4 weeks post-calving. Live weight changed with time, but there was no effect of treatment (P>0.05), whereas cows receiving IB had the lowest mean body condition score and DB the highest (P<0.05). There was no effect of treatment on post-partum DM intake, milk yield or milk fat concentration (P>0.05) with mean values of 21.6 kg/day, 39.6 kg/day and 40.4 g/kg, respectively. Cows receiving IB had a higher plasma vitamin B₁₂ concentration than those receiving any of the other treatments (P<0.001), but there was no effect (P>0.05) of treatment on homocysteine or succinate concentrations, although mean plasma methylmalonic acid concentrations were lower (P=0.019) for cows receiving IB than for Control cows. Plasma β-hydroxybutyrate concentrations increased sharply at calving followed by a decline, but there was no effect of treatment. Similarly, there was no effect (P>0.05) of treatment on plasma non-esterified fatty acids or glucose. Whole tract digestibility of DM and fibre measured at week 7 of lactation were similar between treatments, and there was little effect of treatment on the milk fatty acid profile except for C15:0, which was lower in cows receiving DC than IB (P<0.05). It is concluded that a basal dietary concentration of 0.21 mg Co/kg DM is sufficient to meet the requirements of high yielding dairy cows during the transition period, and there is little benefit from additional Co or vitamin B₁₂.     

Influence of Lime and Phosphate on Nodulation of Soil-Grown Trifolium subterraneum L. by Indigenous Rhizobium trifolii

Previous research had identified four serogroups of Rhizobium trifolii indigenous to the acidic Abiqua soil (fine, mixed, mesic Cumulic Ultic Haploxeroll). Nodulation of subterranean clover (Trifolium subterraneum L.) by two of the serogroups, 6 and 36, was differentially influenced by an application of CaCO₃ which raised the pH of the soil from 5.0 to 6.5. These studies were designed to characterize this phenomenon more comprehensively. Liming the soil with either CaCO₃, Ca(OH)₂, MgO, or K₂CO₃ significantly (P = 0.05) increased the percent nodule occupancy by serogroup 36, whereas the percent nodule occupancy by serogroup 6 was decreased, but the decrease was significant (P = 0.05) only after application of either CaCO₃ or Ca(OH)₂. Application of KH₂PO₄ (25 mg of P kg of soil⁻¹), which did not change soil pH, also significantly (P = 0.05) increased the percent nodule occupancy by serogroup 36. Application of KH₂PO₄ in combination with Ca(OH)₂ produced the same increase in nodule occupancy by serogroup 36 as did individual application of the two materials. Soil populations of serogroup 36 consistently, and in the majority of cases significantly (P = 0.05), outnumbered those of serogroup 6 before planting and after harvest regardless of soil treatment or the outcome of nodulation. Soil chemical and plant analyses provided no evidence that liming was simulating phosphate addition by increasing the availability and subsequent uptake of soil P_i by the subclover plants. Liming did, however, result in a significant transformation (30 to 50 mg of P kg of soil⁻¹) of P_i from the residual soil P_i fraction into an NaOH-extractable organic P fraction during the preplant equilibration period.     

Relationships of Initial Population Densities of Meloidogyne incognita and M. hapla to Yield of Tomato

Microplots 80 × 100 cm, infested with varying initial population densities (P_i) of Meloidogyne incognita or M. hapla, were planted to tomato at two locations. Experiments were conducted in a sandy loam soil at Fletcher, N. C. (mountains) where the mean temperature for May to September is ca 20.7 C, and in a loamy saml at Clayton, N. C. (coastal plain) where the mean temperature for May to Septemher is ca 24.8 C. In these experimentally infested plots, M. incognita and M. hapla caused maximunt yield losses of 20-30%, at lhe mountain site with Pi of 0-12,500 eggs and larvae/500 cm³ of soil. In the coaslal plain, M. incognita suppressed yields up to 85%, and M. hapla suppressed yields up to 50% in comparison with the noninfested control. A part of the high losses at this site apparently was due to M. incognita predisposing tomato to the early blight fungus. In a second experintent, in which a nematicide was used to obtain a range of P_is (with P_i as high as 25,000/50 cm³ of soil) at Fletcher, losses due to M. incognita were as great as 50%, but similar densities of M. hapla suppressed yields by only 10-25%. Approximate threshold densities for both species ranged from 500 to 1,000 larvae and eggs (higher for surviving larvae) for the mountain site, whereas nutnbers as low as 20 larvae/500 cm³ of soil of either species caused signiticant damage in the coastal plain. Chemical soil treatments proved useful in obtaining various initial population densities; however, problems were encountered in measuring effective inoculum after such treatments, especially in the heavier soil.     

外源磷或有机质对板蓝根吸收转运砷的影响

采用土壤培养方法,研究了不同含砷水平土壤中添加外源磷或有机质对砷在板蓝根地下部和地上部累积与分配的影响。结果表明,在外源添加磷或者有机质的情况下,与自然土相比含砷土对板蓝根的生长有一定的促进作用;在自然土(13.4 mg/kg)中,外源磷没有明显影响板蓝根地下部对砷的累积,却显著降低了砷由地下部向地上部的转运,并且添加200 mg P2 O5/kg显著降低了砷在地上部的累积。然而,在含砷土(33.4 mg/kg)中,100 mg P2O5/kg处理显著降低了砷在地下部的累积,但随磷用量的增加反而促进了地下部砷的累积;在添加有机质试验中,10 g/kg的有机质显著降低了自然土中板蓝根地下部和地上部对砷的累积,并且砷的吸收能力也明显下降。在含砷土(23.4 mg/kg)中,添加5 g/kg的有机质不仅降低了砷在板蓝根中的富集,而且降低了其对砷的吸收能力,提高了砷由地下部向地上部的转运,但是随着有机质施用量增至10 g/kg,地下部砷含量及其吸收砷的能力均有一定程度的增大。因此,在砷水平较低的自然土壤上种植板蓝根添加200 mg P2O5/kg和10 g/kg的有机质是控制砷在该草药体内积累的适宜用量,而在砷水平较高的土壤上100 mg P2O5/kg和5 g/kg的有机质是降低板蓝根体内砷累积的适宜用量。     

Effects of beauvericin to mammalian tissue and its production by Austrian isolates ofFusarium proliferatum and Fusarium subglutinans

Austrian isolates ofFusarium subglutinans andFusarium proliferatum were studied for their ability to produce beauvericin, moniliformin and fumonisin B₁ and B₂ under laboratory conditions. Analytical methodology for beauvericin was specially adapted for this task. Our analyses showed that the strains produced beauvericin up to 687 mg /kg maize and moniliformin up to 70 mg/kg. The culture ofF. proliferatum in addition produced fumonisin B₁ and B₂ at levels of 106 and 61 mg/kg,respectively. The preliminary toxicity experiments performed in this study clearly indicated a toxic effect of beauvericin on the contractility of mammalian smooth muscle and thus on mammalian cells.     

Anaerobic Mineralization of Quaternary Carbon Atoms: Isolation of Denitrifying Bacteria on Dimethylmalonate

The microbial capacity to degrade simple organic compounds with quaternary carbon atoms was demonstrated by enrichment and isolation of five denitrifying strains on dimethylmalonate as the sole electron donor and carbon source. Quantitative growth experiments showed a complete mineralization of dimethylmalonate. According to phylogenetic analysis of the complete 16S rRNA genes, two strains isolated from activated sewage sludge were related to the genus Paracoccus within the α-Proteobacteria (98.0 and 98.2% 16S rRNA gene similarity to Paracoccus denitrificans^T), and three strains isolated from freshwater ditches were affiliated with the β-Proteobacteria (97.4 and 98.3% 16S rRNA gene similarity to Herbaspirillum seropedicae^T and Acidovorax facilis^T, respectively). Most-probable-number determinations for denitrifying populations in sewage sludge yielded 4.6 × 10⁴ dimethylmalonate-utilizing cells ml⁻¹, representing up to 0.4% of the total culturable nitrate-reducing population.     

Linking activity,composition and seasonal dynamics of atmospheric methane oxidizers in a meadow soil

Microbial oxidation is the only biological sink for atmospheric methane. We assessed seasonal changes in atmospheric methane oxidation and the underlying methanotrophic communities in grassland near Giessen (Germany), along a soil moisture gradient. Soil samples were taken from the surface layer (0–10 cm) of three sites in August 2007, November 2007, February 2008 and May 2008. The sites showed seasonal differences in hydrological parameters. Net uptake rates varied seasonally between 0 and 70 μg CH₄ m⁻² h⁻¹. Greatest uptake rates coincided with lowest soil moisture in spring and summer. Over all sites and seasons, the methanotrophic communities were dominated by uncultivated methanotrophs. These formed a monophyletic cluster defined by the RA14, MHP and JR1 clades, referred to as upland soil cluster alphaproteobacteria (USCα)-like group. The copy numbers of pmoA genes ranged between 3.8 × 10⁵–1.9 × 10⁶ copies g⁻¹ of soil. Temperature was positively correlated with CH₄ uptake rates (P<0.001), but had no effect on methanotrophic population dynamics. The soil moisture was negatively correlated with CH₄ uptake rates (P<0.001), but showed a positive correlation with changes in USCα-like diversity (P<0.001) and pmoA gene abundance (P<0.05). These were greatest at low net CH₄ uptake rates during winter times and coincided with an overall increase in bacterial 16S rRNA gene abundances (P<0.05). Taken together, soil moisture had a significant but opposed effect on CH₄ uptake rates and methanotrophic population dynamics, the latter being increasingly stimulated by soil moisture contents >50 vol% and primarily related to members of the MHP clade.     

Analysis of Crop Losses in Tomato Due to Pratylenchus penetrans

The effects of Pratylenchus penetrans upon yields of ''Veebrite'' tomato were studied at initial soil population densities (P_i) of 360, 2,010, 4,580, and 14,360 nematodes/kg of soil in 20-cm (i.d.) clay-tile microplots. The lowest P_i appeared to stimulate fruit production. Higher P_i''s suppressed fruit production (total weight of marketable tomatoes and numbers of intermediate- and large-sized fruits), in comparison to control yields, the highest P_i resulted in 38% fewer fruits which weighed 44% less. These losses were at least partly due to a delay in fruit ripening, caused by the nematodes, which did not become apparent until the fourth week. Nematode populations in the soil increased at all but the highest P_i; final populations were around 7,000/kg of soil. Nematode populations in roots ranged from 230-590/gm of root at the completion of the experiment. Nematode control by fumigation would definitely be warranted at soil population densities of 2,000/kg or higher; with 500-2,000/kg, the decision to fumigate would depend on soil type and economic and hiological factors.     

Seasonal fluctuations in the population of denitrifying and N2-fixing bacteria in an acid soil of a Norway spruce forest

The seasonal fluctuations in the concentration of cultured denitrifying and N₂-fixing bacteria were followed in an ammonium fertilised and a control soil of a Norway spruce forest near Villingen/Black Forest from December 1994 to August 1998. The horizontal distribution of bacteria in three layers was determined by the MPN-method and by molecular probing (colony hybridisation) using specific 0.4–0.7 kb DNA probes for denitrification steps (narG, nirS, nirK and nosZ) and for N₂-fixation (nifH). The data showed that highest bacterial counts and higher numbers of denitrifying and N₂-fixing bacteria were generally detectable in the upper (= 5 cm) soil layer and that their amount decreased with soil depth. The concentration of these cultured bacteria showed seasonal fluctuations with highest numbers in autumn/winter/early spring and with low counts in summer. Denitrifying and N₂-fixing bacteria amounted to less than 10% of the total number of cultured bacteria determined by the MPN-method. Fertilisation with ammonium did not cause a shift in the population of these bacteria. These findings were corroborated by hybridisation experiments with genomic DNA isolated from the different layers. Strongest DNA–DNA hybridisation band intensities were obtained in the upper soil layer and their intensities decreased with soil depth. Soil samples from Villingen assayed in the laboratory produced N₂O (in dependence of nitrate and C₂H₂ added to the vessels) and utilised this gas with higher activities in the assays with the fertilised soil. It is concluded that molecular techniques can successfully be applied for assessing seasonal fluctuations of bacterial populations in soil. Relative abundance of denitrifying and N₂-fixing bacteria can be determined from experiments with DNA isolated from soils. Attempts to transform these results to the total population of soil bacteria on a single cell basis are faced with many uncertainties.     

Effect of Toxic Metals on Indigenous Soil β-Subgroup Proteobacterium Ammonia Oxidizer Community Structure and Protection against Toxicity by Inoculated Metal-Resistant Bacteria

Contamination of soils with toxic metals is a major problem on military, industrial, and mining sites worldwide. Of particular interest to the field of bioremediation is the selection of biological markers for the end point of remediation. In this microcosm study, we focus on the effect of addition of a mixture of toxic metals (cadmium, cobalt, cesium, and strontium as chlorides) to soil on the population structure and size of the ammonia oxidizers that are members of the beta subgroup of the Proteobacteria (β-subgroup ammonia oxidizers). In a parallel experiment, the soils were also treated by the addition of five strains of metal-resistant heterotrophic bacteria. Effects on nitrogen cycling were measured by monitoring the NH₃ and NH₄⁺ levels in soil samples. The gene encoding the α-subunit of ammonia monooxygenase (amoA) was selected as a functional molecular marker for the β-subgroup ammonia oxidizing bacteria. Community structure comparisons were performed with clone libraries of PCR-amplified fragments of amoA recovered from contaminated and control microcosms for 8 weeks. Analysis was performed by restriction digestion and sequence comparison. The abundance of ammonia oxidizers in these microcosms was also monitored by competitive PCR. All amoA gene fragments recovered grouped with sequences derived from cultured Nitrosospira. These comprised four novel sequence clusters and a single unique clone. Specific changes in the community structure of β-subgroup ammonia oxidizers were associated with the addition of metals. These changes were not seen in the presence of the inoculated metal-resistant bacteria. Neither treatment significantly altered the total number of β-subgroup ammonia-oxidizing cells per gram of soil compared to untreated controls. Following an initial decrease in concentration, ammonia began to accumulate in metal-treated soils toward the end of the experiment.