Storage Pit Research Articles

New archaeobotanical finds of Isatis tinctoria L. (woad) from Iron Age Gaul and a discussion of the importance of woad in ancient time

Although chemical analyses of textile remains have traced the use of Isatis tinctoria L. (woad) back to the Neolithic period, archaeobotanical remains of the plant are scarce in north-western Europe, especially in France. A new discovery in the rural settlement of Roissy, north of Paris, raises the question of local cultivation of woad from at least the fifth–fourth century b.c. (La Tene A/B1) in northern Gaul. The plant assemblage comes from the filling of a storage pit, which also included a wide variety of cultivated plants. These data represent a valuable contribution to the study of the circumstances of the adoption of woad as a new crop.

Airflow characteristics at the surface of manure in a storage pit affected by ventilation rate, floor slat opening, and headspace height

To inform the modelling ammonia of emissions from manure surfaces and provide basic knowledge of the characteristics of airflow at the emission surface, laboratory experiments were performed using a scale model of a growing/finishing pig house with water in the pit and a clean slatted floor with various opening areas: 100%, 33.3% and 16.7%. At 100% opening area the headspace formed an integral part of the room airspace and this configuration was used as the reference treatment. The pig house model had two sidewall inlets and exhaust in the middle of the ceiling. The effects of room ventilation rate, slatted floor opening and headspace height in slurry pit on air velocity, turbulence intensity (Ti) and airflow pattern at manure surface were investigated. The mean air velocity at manure surface increased as ventilation rate increased with a constant inlet opening. Increasing the opening ratio of the slatted floor increased the air exchange rate in the slurry pit, resulting in a higher air velocity above manure surface. For 33.3% and 16.7% floor slat openings, the mean air velocity at the manure surface decreased as headspace height increased and this resulted in an increased mean Ti above the manure surface for 50 mm and 82 mm headspace heights, respectively. However, no significant differences were found in the mean Ti between four ventilation rates for 26 mm headspace height. Tests using smoke visualisation showed that the supply air travelled longer distances parallel to the manure surface at lower headspace heights than at higher heights before returning to the room space. Ammonia emission results from previous experiments can be explained by using the results of measurements of air velocity and Ti. A statistical model was developed to calculate the mean air velocity as a function of ventilation rate, opening ratio of the slatted floor and headspace height in the slurry pit (coefficient of determination R2 = 0.97). The mean air velocity was more sensitive to the ventilation rate than to the slatted floor opening ratio and the headspace height in the pit. Moreover, the mean air velocity was much more sensitive to variations in the ventilation rate at higher ventilation rates than at lower ventilation rates. However, the mean air velocity was much more sensitive at lower floor slat opening ratios and headspace heights than at higher ones.

Robinsoniella peoriensis gen. nov., sp. nov., isolated from a swine-manure storage pit and a human clinical source

A polyphasic taxonomic study was performed on six strains of an unknown Gram-positive, non-motile, spore-forming, short oval to rod-shaped bacterium isolated from a swine-manure storage pit. In addition to these strains, an isolate deposited in the Culture Collection of the University of Göteborg (Sweden) was found to be biochemically related to the manure strains. The major end products of metabolism included acetate and succinate but not butyrate. Comparative 16S rRNA gene sequencing confirmed that all these isolates were closely related to each other and formed a hitherto unknown lineage within the clostridial rRNA XIVa cluster of organisms. On the basis of phylogenetic, biochemical and phenotypic evidence, it is proposed that the unknown bacterium represents a novel genus and species, for which the name Robinsoniella peoriensis gen. nov., sp. nov. is proposed. The type strain of Robinsoniella peoriensis is PPC31T (=CCUG 48729T =NRRL B-23985T).

Archaeological prospecting at the Double Ditch State Historic Site, North Dakota, USA

AbstractA four‐year programme of remote sensing at the Double Ditch State Historic Site, a fortified earthlodge village in the Great Plains of North Dakota, USA, demonstrates the importance of combined prospecting methods for understanding the multidimensional nature of complex settlements. Aerial survey from a powered parachute acquired high‐resolution digital colour and thermal infrared imagery. The former distinguishes houses, borrow pits and ditches from middens and fill areas by changes in vegetation; the latter does the same through temperature variations that also highlight substantial village deposits and century‐old excavations. Magnetic gradiometry reveals two previously unknown fortification systems that vastly increase the settlement's area and projected population to perhaps 2000 individuals. Vast numbers of food storage pits that supported that population are also indicated. Vertical soundings and area surveys of magnetic susceptibility aid in the understanding of storage pit magnetism and anthropogenic soil mounding and removal. A high‐resolution digital model of topography documents surface expressions caused by ditches, houses, borrow pits and mounds; when combined with overlays of geophysical data understanding of remote sensing responses is improved and relationships between large mounds with village defenses are made clear. Ground‐penetrating radar gives insights into mounded midden interior forms and yields details about house interior components, while electrical resistance results improve definition of middens, other depositional areas, houses and borrow pits. This multisensor remote sensing programme reduced excavation costs by allowing a wide variety of archaeological features of interest to be targeted accurately. Excavations confirmed anomaly identifications and established a chronology that documents late fifteenth century origins to an ultimate abandonment about AD 1782. Copyright © 2008 John Wiley & Sons, Ltd.

Ammonia Emissions Affected by Airflow in a Model Pig House: Effects of Ventilation Rate, Floor Slat Opening, and Headspace Height in a Manure Storage Pit

Laboratory experiments were performed to study the influence of airflow on ammonia emissions from pig house slurry in a model growing/finishing pig house with slurry in the pit and a clean slatted floor with various opening areas, 100%, 33.3%, and 16.7%. The 100% opening area meant that the headspace was an integral part of the room air space, and this configuration was used as the reference treatment. The pig house model had two sidewall inlets and exhaust in the middle of the ceiling. The liquid slurry used was from a growing/finishing pig building and consisted of 1% to 2% dry matter, had pH of 8.05, and TAN (total ammonia nitrogen) of 2.38 g/L. Experiments in a model growing/finishing swine barn were conducted to determine the effects of room ventilation rate, slurry pit air exchange rates, slatted floor openings, and pit headspace on ammonia emissions. The results showed that ammonia emission rate increased as ventilation rate increased with a constant inlet opening. Increase in the slatted floor opening ratio increased the air exchange rate in the slurry pit, resulting in a higher ammonia emission rate. Different correlations between the ammonia emission rate and the air headspace height in the slurry pit caused by the type of flow in the boundary layer influenced the ammonia transport from the slurry surface to the ventilation air. A statistical model was developed to calculate the ammonia emission rate as a function of ventilation rate, slatted floor opening ratio, and slurry pit headspace (R2 = 0.93). It was found that the NH3 emission rate was more sensitive to the ventilation rate than to the slatted floor opening ratio and air headspace height in the pit. In addition, the NH3 emission rate was much more sensitive to variations in the ventilation rate at low ventilation rates than at high ventilation rates. Similar sensitivity responses were obtained for both slatted floor opening ratio and air headspace height.

Mode of occurrence and environmental mobility of oil-field radioactive material at US Geological Survey research site B, Osage-Skiatook Project, northeastern Oklahoma

Two samples of produced-water collected from a storage tank at US Geological Survey research site B, near Skiatook Lake in northeastern Oklahoma, have activity concentrations of dissolved 226Ra and 228Ra that are about 1500 disintegrations/min/L (dpm/L). Produced-water also contains minor amounts of small (5–50 μm) suspended grains of Ra-bearing BaSO 4 (barite). Precipitation of radioactive barite scale in the storage tank is probably hindered by low concentrations of dissolved SO 4 (2.5 mg/L) in the produced-water. Sediments in a storage pit used to temporarily collect releases of produced-water have marginally elevated concentrations of “excess” Ra (several dpm/g), that are 15–65% above natural background values. Tank and pit waters are chemically oversaturated with barite, and some small (2–20 μm) barite grains observed in the pit sediments could be transferred from the tank or formed in place. Measurements of the concentrations of Ba and excess Ra isotopes in the pit sediments show variations with depth that are consistent with relatively uniform deposition and progressive burial of an insoluble Ra-bearing host (barite?). The short-lived 228Ra isotope (half-life = 5.76 a) shows greater reductions with depth than 226Ra (half-life = 1600 a), that are likely explained by radioactive decay. The 228Ra/ 226Ra activity ratio of excess Ra in uppermost pit sediments (1.13–1.17) is close to the ratio measured in the samples of produced-water (0.97, 1.14). Declines in Ra activity ratio (excess) with sediment depth can be used to estimate an average rate of burial of 4 cm/a for the Ra-bearing contaminant. Local shallow ground waters contaminated with NaCl from produced-water have low dissolved Ra (<20 dpm/L) and also are oversaturated with barite. Barite is a highly insoluble Ra host that probably limits the environmental mobility of Ra at site B.

Composition of pore water in lake sediments, research site “B”, Osage County, Oklahoma: Implications for lake water quality and benthic organisms

Shallow ground water at US Geological Survey research site B in northeastern Oklahoma is contaminated with NaCl-rich brine from past and present oil production operations. Contaminated ground water provides a potential source of salts, metals, and hydrocarbons to sediment and water of adjacent Skiatook Lake. A former brine storage pit 10 m in diameter that is now submerged just offshore from site B provides an additional source of contamination. Cores of the upper 16–40 cm of lake sediment were taken at the submerged brine pit, near an offshore saline seep, and at a location containing relatively uncontaminated lake sediment. Pore waters from each 2-cm interval were separated by centrifugation and analyzed for dissolved anions, cations, and trace elements. High concentrations of dissolved Cl − in pore waters (200–5000 mg/L) provide the most direct evidence of contamination, and contrast sharply with an average value of only about 37 mg/L in Skiatook Lake. Chloride/Br − mass ratios of 220–240 in contaminated pore waters are comparable to values in contaminated well waters collected onshore. Dissolved concentrations of Se, Pb, Cu and Ni in Cl −-rich pore waters exceed current US Environmental Protection Agency criteria for probable toxicity to aquatic life. At the submerged brine storage pit, the increase of Cl − concentration with depth is consistent with diffusion-dominant transport from deeper contaminated sediments. Near the offshore saline seep, pore water Cl − concentrations are consistently high and vary irregularly with depth, indicating probable Cl − transport by layer-directed advective flow. Estimated annual contributions of Cl − to the lake from the brine storage pit (∼20 kg) and the offshore seep (∼9 kg) can be applied to any number of similar sources. Generous estimates of the number of such sources at site B indicate minimal impact on water quality in the local inlet of Skiatook Lake. Similar methodologies can be applied at other sites of NaCl contamination surrounding Skiatook Lake and elsewhere.

6. Settlement patterns-Social and ritual space in prehistoric Samoa

Abstract This paper explores the extensive prehistoric settlement pattern at the Letolo plantation. Using the results of earlier research we use a correspondence analysis to investigate variation in the settlement pattern, particularly differences between coastal and inland locations. Investigation of archaeological sites in Samoa in the 1960s and 1970s resulted in several suggestions about the prehistoric settlement pattern (Davidson 1969, Davidson 1974:242; Jennings et al. 1982). The first archaeological excavations investigated a variety of sites, and an important conclusion of this research was that prehistoric settlement was established at both coastal and inland locales in early prehistory (at least by c. 2000 BP). It was also found that house pavements were an early component of the settlement sequence, but raised stone and earth platforms/mounds for occupation or ritual space are, to current knowledge, confined to the last millennium (Wallin, Martinsson-Wallin and Clark, this publication). A temporal shift in material culture in Samoa is thereby evident. Roads and stone walls were frequently associated with large platforms/mounds. The roads were often clearly defined by stone walls and connected house hold units. Settlement pattern studies Jennings et al. (1982) based their discussion of Samoan prehistoric settlement patterns on data from ethnohistorical records, extensive archaeological survey data and excavations, which they compared with the layout of the contemporary village of Fa'a'ala on Savai'i. The results of the Letolo archaeological survey were employed to interpret the prehistoric settlement pattern, but other settlements at Mt Olo on Upolu, and the Sapapali'i settlements on Savai'i were also brought into the discussion. Using the ethnohistoric settlement data as a backdrop, Jennings et al. (1982) concluded that prehistoric settlements consisted of a household unit (HHU) made up of a few individual house platforms, with a cooking area separated from the other units by walls or walkways (more than 75% were enclosed by walls), and a possible garden area within the enclosure (Jennings et al. 1982:82). Several HHU grouped around a chief's dwelling unit, which was identified by a larger platform. Collectively these chiefly clusters constituted a unit called pito nu'u (residential wards). Several pito nu'u clusters constituted a larger unit called nu'u (village) with a mala'e (village green) and a fale tele (community house). Larger platforms were identified as a chief's dwelling or a community meeting house, and through the use of statistical methods the Letolo settlement pattern was divided in to five village wards (pito nu'u) by Jennings et al. (1982:84) (Figure 1). Roger Green subsequently put forward a sequence in which the settlement pattern has various phases, but there is strong cultural continuity evident throughout the prehistoric sequence (Green 2002:135-146): 1. Settlement patterns during the period of the decorated Lapita ceramics (c. 2900-2700 BP) 2. Settlement patterns during the period of Polynesian plainware (c.2700-2000/1500? BP) 3. An interval for which settlement pattern evidence is extremely limited (c. 1500-1000 BP) 4. Settlement patterns between 1000 and 200 years ago (c. 1000-200 BP). The earliest archaeological evidence for the settlement pattern came from a house site with Polynesian plainware at Sasoa'a which was dated to c. 1800 BP (Green 2002:138139). The house comprised a principal dwelling (PPN *fale) with its posts (PPN *pou, tulu), and other features including an earth oven (PPN *umu), stone pavement (PPN *paepae), storage pit (PPN *lua) and boundary fence (PPN *lotuqaa). The house layout and features were seen by Green as similar to those of the later household units (HHU), suggesting that there was continuity in the social formations expressed in the Samoan settlement pattern. Green also suggests that Ancestral Polynesian societies were house societies and HHU were tied to a social group (PPN * kainga) 'aiga probably lead by a family elder (PPN * fatu). …

Vagococcus elongatus sp. nov., isolated from a swine-manure storage pit

A polyphasic taxonomic study was performed on an uncharacterized Gram-positive, catalase-negative, elongated coccus-shaped bacterium isolated from a swine-manure storage pit. The bacterium, designated strain PPC9(T), was facultatively anaerobic and had a DNA G+C content of 44.5 mol%. Comparative 16S rRNA gene sequencing indicated that the bacterium represented a novel subline within the genus Vagococcus, close to but distinct from Vagococcus lutrae. Strain PPC9(T) was readily distinguished from the five recognized species of the genus Vagococcus by using biochemical tests and molecular genetic analysis. Based on phylogenetic and phenotypic evidence strain PPC9(T) is considered to represent a novel species of the genus Vagococcus, for which the name Vagococcus elongatus sp. nov. is proposed. The type strain is PPC9(T) (=CCUG 51432(T)=NRRL B-41357(T)).

Using minced horseradish roots and peroxides for the deodorization of swine manure: A pilot scale study

Enzymes that have proven to be capable of removing toxic compounds from water and soil may also be useful in the deodorization of animal manures. Considering that pork production in the US is a $40-billion industry with over half a million workers, odor control to protect air quality in the neighboring communities must be considered an essential part of managing livestock facilities. This pilot scale (20–120 L) study tested the use of minced horseradish ( Armoracia rusticana L.) roots (1:10 roots to swine slurry ratio), with calcium peroxide (CaO 2 at 34 mM) or hydrogen peroxide (H 2O 2 at 68 mM), to deodorize swine slurry taken from a 40,000-gallon storage pit at the Pennsylvania State University’s Swine Center. Horseradish is known to contain large amounts of peroxidase, an enzyme that, in the presence of peroxides, can polymerize phenolic odorants and thus reduce the malodor. Twelve compounds commonly associated with malodor (seven volatile fatty acids or VFAs, three phenolic compounds and two indolic compounds) were used as odor indicators. Their concentration in swine slurry before and after treatment was determined by gas chromatography (GC) to assess the deodorization effect. The pilot scale testing demonstrated a complete removal of phenolic odorants (with a detection limit of 0.5 mg L −1) from the swine slurry, which was consistent with our previous laboratory experiments using 30-mL swine slurry samples. Horseradish could be recycled (reused) five times while retaining significant reduction in the concentration of phenolic odorants. In view of these findings, inexpensive plant materials, such as horseradish, represent a promising tool for eliminating phenolic odorants from swine slurry.

Effects of Gibberellic Acid (GA3) on Sprouting and Quality of Potato Seed Tubers in Diffused Light and Pit Storage Conditions

Effects of Gibberellic Acid (GA3) on Sprouting and Quality of Potato Seed Tubers in Diffused Light and Pit Storage Conditions

White light micrograting multiplexing for high density data storage

Recording of multiplexed microholographic gratings with improved recording volume for high density optical data storage is proposed and demonstrated. By using a hybrid diffractive-refractive objective lens with extended depth of focus, we have achieved a recording beam size of approximately 1 microm and a focal depth of 20 microm. Multiple gratings corresponding to spectral lines within the 400-650 nm spectral band have been successfully multiplexed in a single recording spot or pit of size 1.25 microm on a DuPont photopolymer film using a white light source along with narrowband filters or dispersion elements, thus demonstrating the storage of multiple bits in a single pit. Simultaneous readout of multiple bits in a single storage pit is accomplished with a microspectrometer-type readout head using a white light source.

Dynamics of a Pig Slurry Microbial Community during Anaerobic Storage and Management

The microbial community of a pig slurry on a farm was monitored for 6 months using both molecular and cultural approaches. Sampling was carried out at all the different stages of effluent handling, from the rearing build-up to slurry spreading. Total DNA of each sample was extracted and analyzed by PCR-single-strand conformation polymorphism (SSCP) analysis using primers targeting the 16S rRNA genes from the archaeal and bacterial domains and also the Eubacterium-Clostridium, Bacillus-Streptococcus-Lactobacillus, and Bacteroides-Prevotella groups. A comparison of the SSCP profiles showed that there were rapid changes in the dominant bacterial community during the first 2 weeks of anaerobic storage and that the community was relatively stable thereafter. Several bacterial populations, identified as populations closely related to uncultured Clostridium and Porphyromonas and to Lactobacillus and Streptococcus cultured species commonly isolated from pig feces, remained present and dominant from the rearing build-up to the time of spreading. Enumeration of fecal indicators (enterococci and Escherichia coli) performed in parallel using cultural methods revealed the same trends. On the other hand, the archaeal community adapted slowly during pig slurry storage, and its diversity increased. A shift between two hydrogenotrophic methanogenic Methanobrevibacter populations from the storage pit to the pond was observed. Microorganisms present in pig slurry at the time of spreading could not be detected in soil after spreading by either molecular or cultural techniques, probably because of the detection limit inherent in the two techniques.

Effects of storage methods, storage time and different agro-ecological zones on chemical components of stored sorghum grain in Hararghe, Ethiopia

Sorghum grain stored in traditional underground pits was sampled from seven districts of Hararghe, eastern Ethiopia, representing lowland, intermediate and highland zones, from February to August 2001, and was analysed at the International Livestock Research Institute (ILRI) for changes in chemical composition over time. Samples were also taken from a replicated aboveground bin and pit storage experiment at Alemaya University campus at 2-month intervals from March 2000 to August 2001 and analysed in a similar manner. The effect of geographic location on chemical composition was significant, but there were differences in the sorghum varieties grown. The organic matter (OM) content of grain samples from pits in the lowlands was lower than those from the highlands. The crude protein (CP) and OM contents of samples from the seven districts did not change in 7–9 storage months. The OM content decreased and the CP slightly increased over time in samples from soil pits without any lining material on Alemaya University campus. The OM content decreased from 97.8 to 91.6%; and CP increased from 10.1 to 11.2% in these samples over a 17-month period. Soluble carbohydrate (SCHO) content significantly decreased over time in samples from the districts (from 2.4 to 1.2% by 7 months) and in samples from soil pits on campus (from 2.4 to 1.9% after 7 months and to 0.97% after 17 months). There was no significant change in the organic matter, CP and SCHO contents in samples taken from the cemented aboveground bin, cement- and dung-lined pits at the Alemaya campus, all of which were lined with polythene sheeting. From these data, we conclude that the combination of storage methods, storage period, geographic location and/or sorghum variety affected grain quality. Grain storage in traditional underground pits for long periods does lead to grain deterioration. The use of improved grain storage structures maintains the grain quality and nutritional value of sorghum for a reasonably long period.

The NIOSH Fatality Assessment and Control Evaluation (FACE) Program

The New York Fatality Assessment and Control Evaluation (FACE) program is designed to identify and study fatal occupational injuries in New York State. The New York FACE program is supported by the National Institute for Occupational Safety and Health (NIOSH) and administered by the New York State Department of Health (NYS DOH) in cooperation with Cornell University. New York FACE investigators evaluate information from multiple sources, conduct objective on-site investigations, and then summarize their findings in narrative reports that include recommendations for preventing similar events in the future. These recommendations are distributed to employers, workers, and other organizations as an educational tool for promoting workplace safety. The following case study involved a 53-year-old dairy farm owner who was fatally injured while transferring manure from an underground storage pit to a manure lagoon. At the time of the incident, the farmer was utilizing a manure pump that was connected to a tractor via a power take-off (PTO) shaft. The farmer reached across the unshielded PTO shaft in order to operate a hand crank that adjusted the manure pump chute. As he did this, his clothing became entangled in the PTO shaft, wrapping the farmer's body around the shaft. New York FACE investigators concluded that to help prevent similar incidents from occurring in the future: PTO-powered equipment should not be operated unless the PTO shield is in place and in good condition; Power to equipment should be turned off prior to making mechanical adjustments; Manure handling systems should be designed to facilitate operator safety; Farm workers should be healthy and well rested prior to performing hazardous activities and; Dairy farm workers should be trained in manure handling safety and knowledgeable about other manure hazards.

Bacteroides coprosuis sp. nov., isolated from swine-manure storage pits

Two Gram-negative, anaerobic, non-spore-forming, rod-shaped organisms were isolated from a swine-manure storage pit. Based on morphological and biochemical criteria, the strains were tentatively identified as belonging to the genus Bacteroides but they did not appear to correspond to any recognized species of the genus. Comparative 16S rRNA gene sequencing studies showed that the strains were related closely to each other and confirmed their placement in the genus Bacteroides, but sequence divergence values of >10 % from reference Bacteroides species demonstrated that the organisms from manure represent a novel species. Based on biochemical criteria and molecular genetic evidence, it is proposed that the unknown isolates from manure be assigned to a novel species of the genus Bacteroides, as Bacteroides coprosuis sp. nov. The type strain is PC139T (=CCUG 50528T=NRRL B-41113T).

A new find of macrofossils of feather grass (Stipa) in an Early Bronze Age storage pit at Vliněves, Czech Republic: local implications and possible interpretation in a Central European context

The abundance of Stipa remains in material dated to the Middle Neolithic (ca. 4400–4000 b.c.) from Kujawy (central Poland) and their presence in a storage pit at Vliněves (Czech Republic) dated to the Early Bronze Age (ca. 2300–1600 b.c.) are most probably connected with gathering of the plant. Stipa grains are edible and the whole plant could have been used as insulation, for making mattresses and for a range of similar purposes. Nowadays spikelets of Stipa are used for decoration. They are dangerous to herbivores because of the sharpness of the basal part of the spikelet and the tendency of the awns to unroll in wet conditions. Already in the first half of the 20th century the plant was regarded as a weed of meadows. The gathering and use of Stipa, as suggested by the abundance of its archaeological macro-remains, was most probably prompted by changes in the local environment. These latter arose from intensive human activity, mostly deforestation and grazing by domestic animals, leading to the formation of steppe-like vegetation. This process is documented by a pollen diagram from a peat section located near the Vliněves site.

Characterisation of the microbial diversity in a pig manure storage pit using small subunit rDNA sequence analysis

The microbial community structure of pig manure slurry (PMS) was determined with comparative analysis of 202 bacterial, 44 archaeal and 33 eukaryotic small subunit (SSU) rDNA partial sequences. Based on a criterion of 97% of sequence similarity, the phylogenetic analyses revealed a total of 108, eight and five phylotypes for the Bacteria, Archaea and Eukarya lineages, respectively. Only 36% of the bacterial phylotypes were closely related (⩾97% similarity) to any previously known sequence in databases. The bacterial groups most often represented in terms of phylotype and clone abundance were the Eubacterium (22% of total sequences), the Clostridium (15% of sequences), the Bacillus–Lactobacillus–Streptococcus subdivision (20% of sequences), the Mycoplasma and relatives (10% of sequences) and the Flexibacter–Cytophaga–Bacteroides (20% of sequences). The global microbial community structure and phylotype diversity show a close relationship to the pig gastrointestinal tract ecosystem whereas phylotypes from the Acholeplasma–Anaeroplasma and the Clostridium purinolyticum groups appear to be better represented in manure. Archaeal diversity was dominated by three phylotypes clustering with a group of uncultured microorganisms of unknown activity and only distantly related to the Thermoplasmales and relatives. Other Archaea were methanogenic H 2/CO 2 utilisers. No known acetoclastic Archaea methanogen was found. Eukaryotic diversity was represented by a pluricellular nematode, two Alveolata, a Blastocystis and an Entamoebidae. Manure slurry physico-chemical characteristics were analysed. Possible inhibitory effects of acetate, sulphide and ammonia concentrations on the microbial anaerobic ecosystem are discussed.

Application of group specific amplified rDNA restriction analysis to characterize swine fecal and manure storage pit samples

Group specific amplified ribosomal-DNA restriction analysis was evaluated as a method to rapidly assess microbial community structure in swine fecal and manure storage pit samples. PCR primer sequences were evaluated for their specificity to ribosomal DNA from selected bacterial groups by optimizing annealing temperatures and determining specificity using a set of primer target and non-target organisms. A number of primer sets were identified targeting the following groups: Bacteroides–Prevotella, clostridial clusters I and II, clostridial clusters IX and XI, clostridial clusters XIVa and XIVb, Lactobacillus, Desulfovibrionaceae and Streptococcus–Lactococcus, as well as an universal primer set to represent total populations. Each bacterial group was digested with at least three restriction enzymes. We applied the group specific amplified ribosomal-DNA restriction analysis to swine fecal and manure storage pit samples obtained on two separate occasions. Fecal and manure storage pit samples obtained on the same day were more similar to each other than to any other samples. Results were consistent with 16S ribosomal DNA sequencing data from bacterial isolates and clones obtained from swine feces and manure storage pit. The group specific amplified ribosomal-DNA restriction analysis technique was able to rapid detect gross bacterial community differences among swine fecal and manure storage pit samples and determine groups of interest for more detailed examination.

Atopostipes suicloacale gen. nov., sp. nov., isolated from an underground swine manure storage pit

Phenotypic and molecular genetic studies were performed on an unknown facultative anaerobic, catalase-negative, non-spore-forming, rod-shaped bacterium isolated from a pig manure storage pit. The unknown bacterium was nutritionally fastidious with growth enhanced by the addition of rumen fluid and was phenotypically initially identified as an Eubacterium species. Comparative 16S rRNA gene sequencing studies, however, revealed that the unknown bacterium was phylogenetically distant from Eubacterium limosum (the type species of the genus Eubacterium) and related organisms. Phylogenetically, the unknown species displayed a close association with an uncultured organism from human subgingival plaque and formed an unknown sub-line within a cluster of organisms which includes Alloioccoccus otitis, Alkalibacterium olivoapovliticus, Allofustis seminis, Dolosigranulum pigrum, and related organisms, within the low mol% G+C Gram-positive bacteria. Sequence divergence values of >8% with all known taxonomically recognised taxa, however, clearly indicates the novel bacterium represents a hitherto unknown genus. Based on both phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium from pig manure be classified in a new genus and species, as Atopostipes suicloacale gen. nov., sp. nov. The type strain of Atopostipes suicloacale is PPC79 T=NRRL 23919 T=DSM 15692 T.