Microbiological characterisation of soils : Evaluation of some critical steps in data collection and experimental design

The study of soil microbiota and their activities is central to the understanding of many ecosystem processes such as decomposition and nutrient cycling. The collection of microbiological data from soils generally involves several sequential steps of sampling, pretreatment and laboratory measurements. The reliability of results is dependent on reliable methods in every step. The aim of this thesis was to critically evaluate some central methods and procedures used in soil microbiological studies in order to increase our understanding of the factors that affect the measurement results and to provide guidance and new approaches for the design of experiments. The thesis focuses on four major themes: 1) soil microbiological heterogeneity and sampling, 2) storage of soil samples, 3) DNA extraction from soil, and 4) quantification of specific microbial groups by the most-probable-number (MPN) procedure. Soil heterogeneity and sampling are discussed as a single theme because knowledge on spatial (horizontal and vertical) and temporal variation is crucial when designing sampling procedures. Comparison of adjacent forest, meadow and cropped field plots showed that land use has a strong impact on the degree of horizontal variation of soil enzyme activities and bacterial community structure. However, regardless of the land use, the variation of microbiological characteristics appeared not to have predictable spatial structure at 0.5-10 m. Temporal and soil depth-related patterns were studied in relation to plant growth in cropped soil. The results showed that most enzyme activities and microbial biomass have a clear decreasing trend in the top 40 cm soil profile and a temporal pattern during the growing season. A new procedure for sampling of soil microbiological characteristics based on stratified sampling and pre-characterisation of samples was developed. A practical example demonstrated the potential of the new procedure to reduce the analysis efforts involved in laborious microbiological measurements without loss of precision. The investigation of storage of soil samples revealed that freezing (-20 °C) of small sample aliquots retains the activity of hydrolytic enzymes and the structure of the bacterial community in different soil matrices relatively well whereas air-drying cannot be recommended as a storage method for soil microbiological properties due to large reductions in activity. Freezing below -70 °C was the preferred method of storage for samples with high organic matter content. Comparison of different direct DNA extraction methods showed that the cell lysis treatment has a strong impact on the molecular size of DNA obtained and on the bacterial community structure detected. An improved MPN method for the enumeration of soil naphthalene degraders was introduced as an alternative to more complex MPN protocols or the DNA-based quantification approach. The main advantage of the new method is the simple protocol and the possibility to analyse a large number of samples and replicates simultaneously.

Formation and preservation of pedogenic carbonates in South India, links with paleo-monsoon and pedological conditions: Clues from Sr isotopes, U-Th series and REEs

The influence of the pedogenic and climatic contexts on the formation and preservation of pedogenic carbonates in a climosequence in the Western Ghats (Karnataka Plateau, South West India) has been studied. Along the climosequence, the current mean annual rainfall (MAR) varies within a 80 km transect from 6000 mm at the edge of the Plateau to 500 mm inland. Pedogenic carbonates occur in the MAR range of 500-1200 mm. In the semi-arid zone (MAR: 500-900 mm), carbonates occur (i) as rhick hardpan calcretes on pediment slopes and (ii) as nodular horizons in polygenic black soils (i.e. vertisols). In the sub-humid zone (MAR: 900-1500 mm), pedogenic carbonates are disseminated in the black soil matrices either as loose, irregular and friable nodules of millimetric size or as indurated botryoidal nodules of centimetric to pluricentimetric size. They also occur at the top layers of the saprolite either as disseminated pluricentimetric indurated nodules or carbonate-cemented lumps of centimetric to decimetric size. Chemical and isotopic (Sr-87/Sr-86) compositions of the carbonate fraction were determined after leaching with 0.25 N HCl. The corresponding residual fractions containing both primary minerals and authigenic clays were digested separately and analyzed. The trend defined by the Sr-87/Sr-86 signatures of both labile carbonate fractions and corresponding residual fractions indicates that a part of the labile carbonate fraction is genetically linked to the local soil composition. Considering the residual fraction of each sample as the most likely lithogenic source of Ca in carbonates, it is estimated that from 24% to 82% (55% on average) of Ca is derived from local bedrock weathering, leading to a consumption of an equivalent proportion of atmospheric CO2. These values indicate that climatic conditions were humid enough to allow silicate weathering: MAR at the time of carbonate formation likely ranged from 400 to 700 mm, which is 2- to 3-fold less than the current MAR at these locations. The Sr, U and Mg contents and the (U-234/U-238) activity ratio in the labile carbonate fraction help to understand the conditions of carbonate formation. The relatively high concentrations of Sr, U and Mg in black soil carbonates may indicate fast growth and accumulation compared to carbonates in saprolite, possibly due to a better confinement of the pore waters which is supported by their high (U-234/U-238) signatures, and/or to higher content of dissolved carbonates in the pore waters. The occurrence of Ce, Mn and Fe oxides in the cracks of carbonate reflects the existence of relatively humid periods after carbonate formation. The carbonate ages determined by the U-Th method range from 1.33 +/- 0.84 kyr to 7.5 +/- 2.7 kyr and to a cluster of five ages around 20 kyr, i.e. the Last Glacial Maximum period. The young occurrences are only located in the black soils, which therefore constitute sensitive environments for trapping and retaining atmospheric CO2 even on short time scales. The maximum age of carbonates depends on their location in the climatic gradient: from about 20 kyr for centimetric nodules at Mule Hole (MAR = 1100 mm/yr) to 200 kyr for the calcrete at Gundlupet (MAR = 700 mm/yr, Durand et al., 2007). The intensity of rainfall during wet periods would indeed control the lifetime of pedogenic carbonates and thus the duration of inorganic carbon storage in soils. (C) 2010 Elsevier Ltd. All rights reserved.

Protected species aerial survey data collection and analysis in waters underlying the R-5306A airspace: final report submitted to US Marine Corps, MCAS Cherry Point

To be in compliance with the Endangered Species Act and the Marine Mammal Protection Act, the United States Department of the Navy is required to assess the potential environmental impacts of conducting at-sea training operations on sea turtles and marine mammals. Limited recent and area-specific density data of sea turtles and dolphins exist for many of the Navy’s operations areas (OPAREAs), including the Marine Corps Air Station (MCAS) Cherry Point OPAREA, which encompasses portions of Core and Pamlico Sounds, North Carolina. Aerial surveys were conducted to document the seasonal distribution and estimated density of sea turtles and dolphins within Core Sound and portions of Pamlico Sound, and coastal waters extending one mile offshore. Sea Surface Temperature (SST) data for each survey were extracted from 1.4 km/pixel resolution Advanced Very High Resolution Radiometer remote images. A total of 92 turtles and 1,625 dolphins were sighted during 41 aerial surveys, conducted from July 2004 to April 2006. In the spring (March – May; 7.9°C to 21.7°C mean SST), the majority of turtles sighted were along the coast, mainly from the northern Core Banks northward to Cape Hatteras. By the summer (June – Aug.; 25.2°C to 30.8°C mean SST), turtles were fairly evenly dispersed along the entire survey range of the coast and Pamlico Sound, with only a few sightings in Core Sound. In the autumn (Sept. – Nov.; 9.6°C to 29.6°C mean SST), the majority of turtles sighted were along the coast and in eastern Pamlico Sound; however, fewer turtles were observed along the coast than in the summer. No turtles were seen during the winter surveys (Dec. – Feb.; 7.6°C to 11.2°C mean SST). The estimated mean surface density of turtles was highest along the coast in the summer of 2005 (0.615 turtles/km², SE = 0.220). In Core and Pamlico Sounds the highest mean surface density occurred during the autumn of 2005 (0.016 turtles/km², SE = 0.009). The mean seasonal abundance estimates were always highest in the coastal region, except in the winter when turtles were not sighted in either region. For Pamlico Sound, surface densities were always greater in the eastern than western section. The range of mean temperatures at which turtles were sighted was 9.68°C to 30.82°C. The majority of turtles sighted were within water ≥ 11°C. Dolphins were observed within estuarine waters and along the coast year-round; however, there were some general seasonal movements. In particular, during the summer sightings decreased along the coast and dolphins were distributed throughout Core and Pamlico Sounds, while in the winter the majority of dolphins were located along the coast and in southeastern Pamlico Sound. Although relative numbers changed seasonally between these areas, the estimated mean surface density of dolphins was highest along the coast in the spring of 2006 (9.564 dolphins/km², SE = 5.571). In Core and Pamlico Sounds the highest mean surface density occurred during the autumn of 2004 (0.192 dolphins/km², SE = 0.066). The estimated mean surface density of dolphins was lowest along the coast in the summer of 2004 (0.461 dolphins/km², SE = 0.294). The estimated mean surface density of dolphins was lowest in Core and Pamlico Sounds in the summer of 2005 (0.024 dolphins/km², SE = 0.011). In Pamlico Sound, estimated surface densities were greater in the eastern section except in the autumn. Dolphins were sighted throughout the entire range of mean SST (7.60°C to 30.82°C), with a tendency towards fewer dolphins sighted as water temperatures increased. Based on the findings of this study, sea turtles are most likely to be encountered within the OPAREAs when SST is ≥ 11°C. Since sea turtle distributions are generally limited by water temperature, knowing the SST of a given area is a useful predictor of sea turtle presence. Since dolphins were observed within estuarine waters year-round and throughout the entire range of mean SST’s, they likely could be encountered in the OPAREAs any time of the year. Although our findings indicated the greatest number of dolphins to be present in the winter and the least in the summer, their movements also may be related to other factors such as the availability of prey. (PDF contains 28 pages)

Introduction of collection and distribution programme for the small-scale fisheries in Ondo State

Details are given of a programme for fresh fish collection and distribution in Ondo State, Nigeria. Collection centers, organization and managerial structure, collection scheme, trade system, price determination, management and distribution are described

Recent developments in fish processing and preservation

A review of the literature on fish processing will reveal that most of the important developments have taken place during the last twenty years. Sustained work by teams of scientists in different parts of the world, has not only contributed much to our knowledge of the chemistry and technology of fish but also resulted in revolutionary changes in the methods of preservation and processing of fishery products.

Improved handling and preservation of freshwater giant prawn, Macrobrachium rosenbergii for producing safe and wholesome products

Studies were undertaken to evaluate the quality changes in freshwater giant prawn, Macrobrachium rosenbergii during various storage conditions of handling and preservation and producing safe and quality products. The samples kept in ice immediately after catch with head-on and head-less condition were found to be acceptable for 6 days and 7 days, respectively. Delaying of icing considerably shortened the shelf-life. The pH value increased from 6.36 to 8.0 after 10 days in ice. The initial average TVB-N value of sample increased from below 10 mg/100 g to 25 mg/100 g with the lapse of storage period. The Ca++ ATPase activity in presence of 0.1M KCl slightly decreased at the end of 10 days of ice storage. Immediately after harvest, initial aerobic plate count (APC) was 2.88x10^6 CFU/g which gradually increased to 1.12x10^8 CFU/g after 6 days in ice storage and showed early signs of spoilage. Initial bacterial genera in the prawn iced at 0 hours were comprised of Coryneform (22.21 %), Bacillus (7.40%), Micrococcus (11.11 %), Achromobacter (48.14%), Flavobacterium/Cytophaga (7.40%), Pseudomonas (3.70%) and Aeromonas (3.70%). During ice storage Coryneforms and Bacillus were always dominating along with less prominent ones - Micrococcus, Achromobacter and Flavobacterium. Studies were conducted on the stability of myofibrillar protein of M. rosenbergii under different storage and pH conditions. The influence of a wide range of pH on the remaining Ca++ ATPase activity of M. rosenbergii muscle myofibrils after storage at -20°C for 2 days, at 0°C for 2 days and at 35°C for 30 minutes demonstrated that ATPase activities were lower in acidic and alkaline pH regions and the activity remained relatively high. Mg++ ATPase activities both in presence and absence of Ca++ remained high at neutral pH compared to those of acidic and alkaline region. The solubility of myofibrillar protein decreased gradually both in acidic and alkaline pH regions. The study also examined the bacteriological quality of freshly harvested M. rosenbergii, pond sediment and pond water from four commercial freshwater prawn farms at Fulpur and Tarakanda upazilas in the district of Mymensingh. The study included aerobic plate count (APC), total coliform count, detection, isolation and identification of suspected public health hazard bacteria and their seasonal variation, salt tolerance test, antibiotic sensitivity test of the isolates and washing effect of chlorinated water on the bacterial load in the prawn samples. APC in sediment soil and water of the farm and gill and hepatopancreas of freshly harvested prawns varied considerably among the farms and between summer and winter season. The range of coliform count in water, gill and hepatopancreas ranged between 6 - 2.8x10^2 CFU/ml, 1.2x10^2 - 3.32x10^2 CFU/g and 1.43x10^2 - 3.89 x10^3 CFU/g, respectively. No coliform was detected in pond sediment sample. Suspected health hazard bacteria isolated and identified from pond sediment, water, gill and hepatopancreas included Streptococcus, Bacillus, Escherichia coli, Klebsialla, Salmonella, Staphylococcus, Pseudomonas and Aeromonas. Bacillus, Salmonella and Staphyloccus [sic], and were found to be highly salt tolerant and capable of growing at 10% NaCl. The antibiotic discs with different concentration of antibiotics were used for the sensitivity test. The organisms were found to be most sensitive against Tetracyclin and Gentamycin.

Studies on smoke curing and preservation of oil sardine (Sardinella longiceps)

A method is reported for smoke curing of oil sardine (Sardinella longiceps) by dry salting in the ratio of 1:6 (salt to fish), followed by smoking in the traditional smoke chamber in two stages, (1) at 45°C for 3h hand (2) at 75°C for 2h with smoke generated from coconut husk, wood shavings and saw dust in 2:2:1 proportion. The product obtained had good odour, flavour, golden yellow colour and a shelf-life of 8 weeks at room temperature (26 to 28°C)

Methods of harvesting and preservation of the diatom Chaetoceros calcitrans

Diatom culture and larval feeding experiments were conducted to test the viability and acceptability of preserved algal concentrates. C. calcitrans is characterised by the presence of setae which keep them suspended in cultures and make autoflocculation very difficult. Flocculation was induced by the addition of a floc-forming chemical. Using the optimum conditions, it was possible to harvest the algae within 1-h settling time and with about 84% recovery. The viability of frozen Chaetoceros was determined by actual cell reproduction. Preliminary feeding experiments showed that Chaetoceros can be successfully used as a substitute for fresh diatoms as feed for Penaeus monodon larvae. Simple freezing techniques, with or without the use of protectants has been found convenient for preserving algal concentrates in small volumes for both feeding and culture purposes.

First charge collection and position-precision data on the medium-resistivity silicon strip detectors before and after neutron irradiation up to 2x10(14) n/cm(2)

Test strip detectors of 125 mu m, 500 mu m, and 1 mm pitches with about 1 cm(2) areas have been made on medium-resistivity silicon wafers (1.3 and 2.7 k Ohm cm). Detectors of 500 mu m pitch have been tested for charge collection and position precision before and after neutron irradiation (up to 2 x 10(14) n/cm(2)) using 820 and 1030 nm laser lights with different beam-spot sizes. It has been found that for a bias of 250 V a strip detector made of 1.3 k Ohm cm (300 mu m thick) can be fully depleted before and after an irradiation of 2 x 10(14) n/cm(2). For a 500 mu m pitch strip detector made of 2.7 k Ohm cm tested with an 1030 nm laser light with 200 mu m spot size, the position reconstruction error is about 14 mu m before irradiation, and 17 mu m after about 1.7 x 10(13) n/cm(2) irradiation. We demonstrated in this work that medium resistivity silicon strip detectors can work just as well as the traditional high-resistivity ones, but with higher radiation tolerance. We also tested charge sharing and position reconstruction using a 1030 nm wavelength (300 mu m absorption length in Si at RT) laser, which provides a simulation of MIP particles in high-physics experiments in terms of charge collection and position reconstruction, (C) 1999 Elsevier Science B.V. All rights reserved.

First charge collection and position-precision data on the medium-resistivity silicon strip detectors before and after neutron irradiation up to 2x10(14) n/cm(2)

Test strip detectors of 125 mu m, 500 mu m, and 1 mm pitches with about 1 cm(2) areas have been made on medium-resistivity silicon wafers (1.3 and 2.7 k Ohm cm). Detectors of 500 mu m pitch have been tested for charge collection and position precision before and after neutron irradiation (up to 2 x 10(14) n/cm(2)) using 820 and 1030 nm laser lights with different beam-spot sizes. It has been found that for a bias of 250 V a strip detector made of 1.3 k Ohm cm (300 mu m thick) can be fully depleted before and after an irradiation of 2 x 10(14) n/cm(2). For a 500 mu m pitch strip detector made of 2.7 k Ohm cm tested with an 1030 nm laser light with 200 mu m spot size, the position reconstruction error is about 14 mu m before irradiation, and 17 mu m after about 1.7 x 10(13) n/cm(2) irradiation. We demonstrated in this work that medium resistivity silicon strip detectors can work just as well as the traditional high-resistivity ones, but with higher radiation tolerance. We also tested charge sharing and position reconstruction using a 1030 nm wavelength (300 mu m absorption length in Si at RT) laser, which provides a simulation of MIP particles in high-physics experiments in terms of charge collection and position reconstruction, (C) 1999 Elsevier Science B.V. All rights reserved.

Damage assessment and preservation of suspending system of Yongle-Big-Bell

The Yongle-Big-Bell is an exquisite heritage of ancient China and has more than 600 years history. The long history renders the suspending wooden rack serious damage. Therefore, the security is of our great concern. In order to know if the wooden rack is safe or not for the conventional striking in the festival service, a systemic research work has been done. At first the existing deformation and response to the strike of the beetle were measured, and then calculations using method of material mechanics and finite element analysis were conducted. Based on the results of our research, some concluding remarks and suggestion were given: The Yongle-Big-Bell can be struck regularly without urgent danger of collapse. In view of the existence of serious rotten damage, the repair and protection of wooden rack are pressing.

Sources and preservation of organic matter in Plum Island salt marsh sediments (MA, USA): long-chain n-alkanes and stable carbon isotope compositions

Elemental (TOC, TN, C/N) and stable carbon isotopic (delta(13)C) compositions and n-alkane (nC(16-38)) concentrations were measured for Spartina alterniflora, a C-4 marsh grass, Typha latifolia, a C-3 marsh grass, and three sediment cores collected from middle and upper estuarine sites from the Plum Island salt marshes. Our results indicated that the organic matter preserved in the sediments was highly affected by the marsh plants that dominated the sampling sites. delta(13)C values of organic matter preserved in the upper fresh water site sediment were more negative (-23.0+/-0.3) as affected by the C-3 plants than the values of organic matter preserved in the sediments of middle (-18.9+/-0.8) and mud flat sites (-19.4+/-0.1) as influenced mainly by the C4 marsh plants. The distribution of n-alkanes measured in all sediments showed similar patterns as those determined in the marsh grasses S. alterniflora and T. latifolia, and nC(21) to nC(33) long-chain n-alkanes were the major compounds determined in all sediment samples. The strong odd-to-even carbon numbered n-alkane predominance was found in all three sediments and nC(29) was the most abundant homologue in all samples measured. Both delta(13)C compositions of organic matter and n-alkane distributions in these sediments indicate that the marsh plants could contribute significant amount of organic matter preserved in Plum Island salt marsh sediments. This suggests that salt marshes play an important role in the cycling of nutrients and organic carbon in the estuary and adjacent coastal waters. (C) 2003 Elsevier Ltd. All rights reserved.

The collection and analysis of pre-evacuation times derived from evacuation trials and their application to evacuation modelling

This paper presents data relating to occupant pre-evacuation times from university and hospital outpatient facilities. Although the two occupancies are entirely different, they do employ relatively similar procedures: members of staff sweep areas to encourage individuals to evacuate.However the manner in which the dependent population reacts to these procedures is quite different. In the hospital case, the patients only evacuated once a member of the nursing staff had instructed them to do so, while in the university evacuation, the students were less dependent upon the actions of the staff, with over 50% of them evacuating with no prior prompting. In addition, the student pre-evacuation time was found to be dependent on their level of engagement in various activities.

Collection and analysis of pre-evacuation time data collected from evacuation trials conducted in library facilities in Brazil

Two evacuation trials were conducted within Brazilian library facilities by FSEG staff in January 2005. These trials represent one of the first such trials conducted in Brazil. The purpose of these evacuation trials was to collect pre-evacuation time data from a population with a cultural background different to that found in western Europe. In total some 34 pre-evacuation times were collected from the experiments and these ranged from 5 to 98 seconds with a mean pre-evacuation time of 46.7 seconds