Estimates of the number of species of bacteria per gram of soil vary between 2000 and 8.3 million (Gans et al., 2005; Schloss and Handelsman, 2006). The highest estimate suggests that the number may be so large as to be impractical to test by amplification and sequencing of the highly conserved 16S rRNA gene from soil DNA (Gans et al., 2005). Here we present the use of high throughput DNA pyrosequencing and statistical inference to assess bacterial diversity in four soils across a large transect of the western hemisphere. The number of bacterial 16S rRNA sequences obtained from each site varied from 26 140 to 53 533. The most abundant bacterial groups in all four soils were the Bacteroidetes, Betaproteobacteria and Alphaproteobacteria. Using three estimators of diversity, the maximum number of unique sequences (operational taxonomic units roughly corresponding to the species level) never exceeded 52 000 in these soils at the lowest level of dissimilarity. Furthermore, the bacterial diversity of the forest soil was phylum rich compared to the agricultural soils, which are species rich but phylum poor. The forest site also showed far less diversity of the Archaea with only 0.009% of all sequences from that site being from this group as opposed to 4%–12% of the sequences from the three agricultural sites. This work is the most comprehensive examination to date of bacterial diversity in soil and suggests that agricultural management of soil may significantly influence the diversity of bacteria and archaea.

The activity of ammonia-oxidizing archaea (AOA) leads to the loss of nitrogen from soil, pollution of water sources and elevated emissions of greenhouse gas. To date, eight AOA genomes are available in the public databases, seven are from the group I.1a of the Thaumarchaeota and only one is from the group I.1b, isolated from hot springs. Many soils are dominated by AOA from the group I.1b, but the genomes of soil representatives of this group have not been sequenced and functionally characterized. The lack of knowledge of metabolic pathways of soil AOA presents a critical gap in understanding their role in biogeochemical cycles. Here, we describe the first complete genome of soil archaeon Candidatus Nitrososphaera evergladensis, which has been reconstructed from metagenomic sequencing of a highly enriched culture obtained from an agricultural soil. The AOA enrichment was sequenced with the high throughput next generation sequencing platforms from Pacific Biosciences and Ion Torrent. The de novo assembly of sequences resulted in one 2.95 Mb contig. Annotation of the reconstructed genome revealed many similarities of the basic metabolism with the rest of sequenced AOA. Ca. N. evergladensis belongs to the group I.1b and shares only 40% of whole-genome homology with the closest sequenced relative Ca. N. gargensis. Detailed analysis of the genome revealed coding sequences that were completely absent from the group I.1a. These unique sequences code for proteins involved in control of DNA integrity, transporters, two-component systems and versatile CRISPR defense system. Notably, genomes from the group I.1b have more gene duplications compared to the genomes from the group I.1a. We suggest that the presence of these unique genes and gene duplications may be associated with the environmental versatility of this group.

Agricultural land management, such as fertilization, liming, and tillage affects soil properties, including pH, organic matter content, nitrification rates, and the microbial community. Three different study sites were used to identify microorganisms that correlate with agricultural land use and to determine which factors regulate the relative abundance of the microbial signatures of the agricultural land-use. The three sites included in this study are the Broadbalk Experiment at Rothamsted Research, UK, the Everglades Agricultural Area, Florida, USA, and the Kellogg Biological Station, Michigan, USA. The effects of agricultural management on the abundance and diversity of bacteria and archaea were determined using high throughput, barcoded 16S rRNA sequencing. In addition, the relative abundance of these organisms was correlated with soil features. Two groups of microorganisms involved in nitrogen cycle were highly correlated with land use at all three sites. The ammonia oxidizing-archaea, dominated by Ca. Nitrososphaera, were positively correlated with agriculture while a ubiquitous group of soil bacteria closely related to the diazotrophic symbiont, Bradyrhizobium, was negatively correlated with agricultural management. Analysis of successional plots showed that the abundance of ammonia oxidizing-archaea declined and the abundance of bradyrhizobia increased with time away from agriculture. This observation suggests that the effect of agriculture on the relative abundance of these genera is reversible. Soil pH and NH3 concentrations were positively correlated with archaeal abundance but negatively correlated with the abundance of Bradyrhizobium. The high correlations of Ca. Nitrososphaera and Bradyrhizobium abundances with agricultural management at three long-term experiments with different edaphoclimatic conditions allowed us to suggest these two genera as signature microorganisms for agricultural land use.

et al., 1998). Some EAA fields had as much as 300 cm of soil above the limestone bedrock when they were Sugarcane (Saccharum spp.) in Florida is increasingly exposed to first drained and used for agriculture. Depth of soil to periodic floods and high water tables for extended durations. We bedrock varies, but a small number of sugarcane fields evaluated the effects of periodic flooding, followed by drainage, on morphological characteristics and cane and sugar yields of two sugar-now have less than 40 cm of soil (Shih et al., 1998). cane genotypes. From 2000-2002, experiments were conducted in Second, for every centimeter of rainfall, the water in lysimeters filled with Pahokee muck soil. Flooding was imposed for the soil profile of EAA Histosols rises about 10 cm 7 d during five, nine, and nine 21-d cycles in 2000, 2001, and 2002, (Glaz et al., 2002). Finally, there are regulated and volrespectively. Cycles commenced when sugarcane leaves covered the untary limits on pumping from farm ditches to public rows and were discontinued in mid-October. Water table depths durcanals as a means of reducing P discharge to the natuing the 14-d drainage period of each cycle were 16, 33, or 50 cm. A ral Everglades. fourth treatment was maintained continuously at a 50-cm water table The issues of soil subsidence and P discharge also depth. Genotype CP 95-1429 yields were not affected by water table provide incentives to maintain yields under high water or flooding. For CP 95-1376 in periodic-flooding treatments, lowering tables and periodic flooding. The primary cause of subsithe water table in 1-cm increments increased cane and sugar yields by 0.16 and 0.02 kg m Ϫ2 , respectively, in 2000 and 0.25 and 0.03 kg dence in the EAA is microbial oxidation (Tate, 1980). m Ϫ2 , respectively, in 2001. Water table depth during drainage did not The factor that most influences the rate of microbial affect CP 95-1376 yields in 2002, perhaps because of a longer duration oxidation is depth of water table in the soil profile. between planting and initial flooding in 2002. Each day of flooding Therefore, the rates of oxidation and subsidence are reduced cane and sugar yields of CP 95-1376 by 0.17 and 0.02 kg m Ϫ2 , directly proportional to the depth of the water table. respectively, in 2000 and by 0.21 and 0.03 kg m Ϫ2 , respectively, in Halving the distance between the water table and the 2002. Flooding might not have reduced yields of CP 95-1429 becausesoil surface has been shown to halve the rate of subsiof its ability to form aerenchyma in the stalks before exposure to dence (Snyder et al., 1978).flooding. Such genotypes should be able to tolerate flooding for at

No abstract

No abstract

Minimum tillage may alter soil P fractions through the application of P fertilizers and the deposition of organic matter on the surface rather than being incorporated into the soil. This study was conducted to determine whether no‐tillage (NT) systems affected soil organic and inorganic P fractions and the transformation of P from residues applied to soils. Surface soils (0–2 cm) under NT and conventional tillage (CT) were sampled from three long‐term research sites. Inorganic and organic P was measured in the NaHCO3, microbial, NaOH, NaOH after sonication, HCl, and residual fractions extracted sequentially. Soybean (Glycine max L.) residues labeled with 33P were added to soils, incubated, and extracted periodically, and 33P was counted in the different P fractions. Levels of 31P in NT were higher in some of the fractions compared with CT; however, there was no consistency in 31P fractionation across soil types due to tillage in any of the inorganic and organic fractions. At the start of incubation, 56 to 82% of the applied 33P was extracted in the resin fraction in the three soils. Resin‐33P followed a three‐parameter single exponential decay model with a corresponding increase in other pools depending on soil. The increase in these pools followed a quadratic model in the three soils. By the end of the incubation period, the NaOH fraction accounted for the majority of the 33P released from the labile resin pool. An increase in the calcium phosphate pool occurred in the calcareous soil. Tillage had no effect on the fate of 33P released from soybean residues during the incubation period.

No abstract