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Soil microorganisms immobilize and mineralize various elements to satisfy their growth requirements. The subsequent turnover of microbial biomass also releases several mineral elements. The elements may be released as a result of organic matter decomposition (e.g. during the process of mineralization, ammonification, etc.) or through biological weathering. Other transformations may involve oxidation and reduction of various inorganic ions and compounds which are mostly catalyzed by chemoautotrophic bacteria during oxidation of ammonium, nitrite, sulphur, iron, etc. Such oxidations may also release energy for microbial growth.

Introduction

Phosphorus is only second to nitrogen as a mineral nutrient required for plants, animals and microorganisms. It is a major constituent of nucleic acids in all living systems essential in the accumulation and release of energy during cellular metabolism. Phosphorus is found in soil, plants and microorganisms in number of organic and inorganic compounds. It is the second major inorganic nutrient after nitrogen in term of quantitative requirement for both crop plants and microorganisms. This element may be added to soil in the form of chemical fertilizers, or it may be incorporated as leaf litter, plant residues or animal remains. In cultivated soils it is present in abundance (i.e. 1100 kg/ha), but most of which is not available to plants, only 15% of total soil phosphorus is in available form. Thus, phosphorus occupies a critical position both in plant growth and in the biology of soil.

Introduction

In soil, microorganisms influence not only the availability of carbon and nitrogen, which are important constituents of plants, but also of sulfur (S), phosphorus and many other trace elements for plant absorption. Sulphur is found widely distributed and considered as tenth most abundant element in the nature. Sulfur is considered as an essential element for survival of plant and animals and found as gypsum (CaSO₄.2H₂O), pyrite (FeS₂) and other combined form and also in elemental form (S⁰) in the nature. The requirement of sulphur by plant is comparatively less than the primary nutrients, hence sulfur is recognised as ‘secondary’ nutrient. 

The planet earth harbors a total population of 7,530,687,482 (as on 7^th September 2017 at 1345hrs) in which Asia and Africa share 4,486,207,286 and 1,252,251,830, respectively. In majority of the countries in Asia and Africa surveillance programs for detection and source tracking of human health hazard bacteria in foods is scant and in some cases do not exist. Hence, the task is much more complicated especially catering to needs of food, nutritional security and microbial safety of foods of more than 5,738,459,116 or 76.2 % of the total population of the world. The continued occurrence of foodborne illness is not evidence of the failure of our food safety system. In fact, many of our prevention and control efforts have been and continue to be highly effective. In advanced countries like US where food supply is one of the safest in the world, however, significant food borne illness continues do occur. Despite great strides in the area of microbiological food safety, much remains to be done.

Food-borne disease outbreaks are defined as the occurrence of 2 or more cases of a similar illness resulting from ingestion of a common food or observed number of cases of a particular disease exceeds the expected number. These can be confirmed (when at least one causal agent is identified) or suspected (based on clinical and epidemiological information). Although most cases are sporadic, these diseases draw attention to themselves due to outbreaks, thorough investigation of which can help in identifying control measures.Annual burden of foodborne diseases in the WHO South- East Asia Region includes more than: 150 million illness, 175 000 deaths, 12 million DALYs (Source: FERG Report 2010).

4.1 Introduction
At the moment of secretion in the udder, milk is sterile; however, it is contaminated by bacteria before it is extracted from the udder. With the exception of mastitis, the bacteria are generally innocuous and restricted at this juncture. Microorganisms may contaminate the milk further during milking, handling, storage, and other pre-processing activities. The bacteria have the potential to either enhance the quality of milk or cause it to deteriorate. Some of the beneficial bacteria, particularly the lactic acid bacteria, are referred to as probiotics. These probiotics are gaining a more prominent position in nutraceutical dairy and other food products, which provide consumers with health benefits such as the control of diarrhoea, antihypertensive, hypocholesterolemia, immunostimulatory, and anticarcinogenic properties.

4.2 Lactic acid bacteria
This particular group of bacteria is capable of homofermentation, which is the process of fermenting lactose to lactic acid, and heterofermentation, which is the process of generating a high number of end products. They are commonly present in milk and are also used as starter cultures in the production of cultured dairy products, such as yoghurt.

Introduction

Numerous characteristics of food determine its acceptability to consumers and to regulatory officials. Before accepting a food for consumption, it must be attractively presented, must have desirable odour and flavour characteristics and other qualities and must be free from potential pathogens or their toxic products. The ultimate nutritive qualities, flavour and appearance have been preserved and no harmful organisms or substances are present to affect the consumer adversely. If the quality of the product is good, its keeping quality is also likely to be substantial. Conversely, there are more chances of spoilage of an inferior quality food product during storage.

1. Introduction

Fruits and vegetables have been an integral part of man’s diet from immemorial times. Fruits are the portions of plants that bear seeds, while vegetables are the edible components of a plant, including the leaves, stalks, roots, tubers, bulbs, flowers and seeds. These can be eaten raw or cooked. Fruits and vegetables can be preserved for short-term intervals under refrigeration, with or without receiving a minimal treatment like slicing, chopping, shredding or peeling. Fresh produce may also be irradiated or packaged in controlled or modified atmosphere in films for short-term storage. Long-term preservation includes canning, juicing, drying and addition of preservatives. Food contamination with hazardous biological agents remains a worldwide challenge in food safety and nutrition (Kenny 2002; Schlundt 2002; Tauxe et al 1997). Microorganisms form part of the epiphytic flora of fruits and vegetables and many will be present at the time of consumption. Production practices, growth conditions and the location of the edible part during growth (soil, soil surface, aerial part) will in combination with intrinsic, extrinsic, harvesting and processing factors affect their microbial status at the time of consumption. Man-made sources may be directly from farm laborers and from the equipment used for harvesting or storage. The types of microorganisms on fruits and vegetables would also vary with the orchards, vineyards or growing fields. The resident microflora normally subsists on the slight traces of carbohydrates, proteins and inorganic salts that dissolve in the water exuding from or condensing on the epidermis of the host. The numbers of bacteria present will vary depending on seasonal and climatic variation and may range from 104 to 108 per gram. The inner tissues of fruits and vegetables are usually regarded as sterile (Lund 1992). However bacteria can be present in low numbers in the insides of the fruits and vegetables as a result of the uptake of water through certain irrigation or washing procedures.

In the last decade or so, the problem of determining the microbial content and their activities in dairy products has been under close scrutiny. The dairy industries still adopt the dye reduction test because it is cheap, simple and satisfactory. However, other new techniques have been introduced along with some modifications in traditional tests. The microbiological quality must be maintained. To assess the bacterial content and their activities in dairy products, various methods are available for the microbiological testing of milk. The specific tests should be chosen as per the application and other factors like cost etc. On the basis of public health and economic consideration it is necessary to test microbiological quality of milk at a number of points along the chain from producer to consumer which includes - raw milk supply, bulk milk arriving at processors premises, monitoring bulk milk during storage prior to processing and monitoring the procession & the quality control of finished products. The techniques for estimating bacterial numbers in raw material are divided into two categories.

Introduction

In this microbiology report, we delve into the intricate realm of bacterial isolation and identification, exploring the fundamental processes that unlock the mysteries of microbial worlds. From the methods employed for isolating bacterial strains to the intricate techniques of identification, this report aims to provide a comprehensive understanding of the crucial role microbiology plays in unraveling the secrets of these microscopic organisms. Join us on a journey through the principles and applications that form the backbone of bacterial isolation and identification in the fascinating field of microbiology.

This chapter introduces the microbiological characteristics of eggs and egg products, beginning with the egg's natural physical and chemical defenses against microorganisms. It examines routes of contamination, spoilage microorganisms and spoilage patterns, with particular emphasis on Salmonella Enteritidis and its public-health significance. Other pathogens of concern and the distinctive microbiology of processed egg products are also considered. The chapter discusses microbiological testing, indicator organisms, contamination control and predictive microbiology, providing a foundation for designing effective safety systems throughout the egg value chain.

1. Bacteria intoxication - already formed bacteria not live bacteria

2. Bacterial infection consumption of live bacteria

3. Neuro toxin produced by C. botulinum

4. Listeria identified by the serotyping

5. Fishery product have type E, C. botulinum

6. S. aureus produced entiro toxin

7. S. aureus is heat resistant but not active in pasteurization

8. E. coli-0157:H7

9. Salmonella should be below 105/g

10. Septicemia can occur due to the salmonella

11. L. monocytogens should be 10/ g

Microorganism is a collective term for all living organisms, which are not visible to the eye, and occupy an intermediate position between the vegetable and animal kingdoms. They are found every where in the atmosphere, in water and in the soil and, as they break down organic materials, they play a very important role in the cycle of the nature.

There are thousands of species which are important to the life and economic structure of the human race. For example, certain species form simple chemical elements during the break down of dead organic material which plants can use again. They increase soil fertility and crop production which results in more food.

Other species are present, and essential, in animal intestines, helping in the digestion of food.

Some microorganisms are used in many food processes, e.g. dahi, yoghurt, cheese, pickles, beer and wine as well as in the acid production to preserve foods. There are microorganisms that produce toxic substances which kill other organisms, e.g. the mould penicillium which produces the substance penicillin.

Many microorganisms cause diseases in animals and plants with a subsequent reduction in the nation’s food supply, whereas others cause food deterioration such as mouldy foods, tainted foods, etc.

A. Enumeration of Different Microflora of Soil
Introduction
Agriculturally, soil is the region which supports the plant life by providing mechanical support and nutrients required for growth. From the microbiologist view point, soil is one of the most dynamic sites of biological interactions in the nature. Soil is an admixture of five major components viz. organic matter, mineral matter, soil-air, soil water and soil microorganisms/living organisms. The amount/ proposition of these components varies with locality and climate.

The soil organisms are broadly classified in two group’s viz. soil flora and soil fauna, the detailed classification of which is as follows.
1) Soil flora
a) Microflora Bacteria, Fungi, Molds, Yeast, Mushroom, Actinomycetes, Streptomyces, Algae e.g. BGA, Yellow Green algae, Golden brown algae.
b) Macroflora

The basic methods for wastewater sewerage (collection, treatment, and disposal) are as follows:

• Off-site sewerage
• Separate sewerage system
• Combined sewerage system
• On-site sewerage

Many nations have implemented separate sewage systems that transmit sewage and storm water through separate pipelines in order to separate the two. Storm water often does not contribute to a wastewater treatment facility (WWTP). Domestic sewage contains 99.9% or more water. The remaining portion is made up of bacteria

Life on Earth is dependent on microorganisms for many essential services. Microbes are intimate partners in global agriculture by way of mobilization of nutrients, antagonism against pathogens and exploitation of plant- microbe interactions and optimization of plant microbiome allows farmers to apply less chemical fertilizers and pesticides, and improving plant growth and yield for sustainable development.

India has 2.4% of land area of world and 8.1% global species diversity. India has 7500 km long coast line in nine states and three union territories. About 14% of Indian population (17 crores) lives in coastal area. In 10.78 million ha of coastal ecosystem, rice is the major coastal crop. Coastal rice accounts for 15% of total area and production of India. Coconut, cashew, areca nut, spices, plantation and fruit crops are the other important coastal crops. The east coast in four states (Tamil nadu, Andhra Pradesh, Orissa, West Bengal) and one union territory (Pondicherry) has sandy coast and plains with medium to high rainfall (100-250 cm), and hot humid climate. It has marshy lands and mangroves. The west coast in five states (Kerala, Karnataka, Goa, Maharashtra, Gujarat) and two union territories (Diu and Daman, Dadar and Nagarhaeli) has fertile sandy plains with high rainfall (250-300 cm) and hot humid climate suitable for horticulture and plantation crops. Western Ghats near west coast is a hot spot with high biodiversity. ICAR established the Central Coastal Agriculture Research Institute (CCARI) at Goa in 2015 to carry out research on coastal agricultural crops.

Soil salinity in coastal regions is not only a soil type character, but also due to low quality irrigation water. The plant associated microorganisms “Plant microbiome” play a significant role in conferring resistance to soil salinity. The endophytic bacteria- rhizobium, rhizobacteria- azospirillum, azotobacter, phosphobacteria, PGPR bacteria, cyanobacteria, symbiotic fungi- ecto and endo mycorrhiza, alleviate the impact of soil salinity. Minimal microbiome for plants is the key determinant of plant health and productivity. The plant- microbe interactions are of three types: (i) Positive: Beneficial organisms- nitrogen fixers, phosphobacteria, mycorrhiza; (ii) Negative: Harmful organisms - plant pathogens; (iii) Neutral: Transient organisms. Millions of microbes inhabit plants, form complex ecological communities to improve plant growth, crop quality and productivity.

Abstract

Cow and buffalo milk is the major source milk worldwide contributing 81 and 15% of total milk production respectively. However, milk from animals like goat, sheep, camel, donkey, yak etc also contribute to human nutrition and health in different parts of world. These milks are source of staple traditional product and considered as delicacy in parts of Europe, UK, USA etc. The microbiota of raw milk and fermented milks, cheeses, made from raw milk is complex. These microorganisms have immense role in determining quality and safety of the subsequent product made from these milks as they may be responsible in spoilage and reducing shelf life, causing human health issues, also contribute to development of flavor and aroma formation, texture development, ripening cheese. Different factors like host, stage of lactation etc. affect the composition of microbiota present in the milks and methods like cultural and culture independent methods metagenomic analysis have been done to determine the microbial community present in the milk.

Introduction

Non- cow and non-buffalo milks such as milks from goat, sheep, camel, donkey, yaks etc. are one of the important sources of nutrition in different parts of the world. In Mongolia, the highlands of the Afghanistan and Pakistan, Himalayas in India, Nepal, and Bhutan, Tibetan Plateau and in the Mountains China yak milk is the only source of milk. Cheese made from sheep and goat milk are categorized as gourmet food and many times regarded as protected designation of origin (PDO) status. Camel milk is used for medicinal food and donkey milk is suitable for children, aged people due to its hypo allergenic properties. These milks and milk products like cheese, naturally fermented milks and yoghurt are staple traditional foods in different parts of the world.

Domestication of animals was followed by the provision of shelters for protection which also modified the climate to suit the species housed for improving the productivity and reproductive efficiency. Climate is the long term average condition of the meteorological variables in a given region. The climate is divided into macro climate and micro climate. Macro climate is the general large scale climatic conditions of the open atmosphere in a large area. Micro-climate is the climatic conditions directly surrounding the animal or the physical environment in the immediate vicinity of the animal. The environment includes all the combination of conditions under which the animal lives. The immediate variables that affect the production and reproduction of animals are its micro climatic variables. The animals have requirements of their own. The environment influences where and how animal lives. Domestication has resulted in man dictating where and how animal lives. Thus breeds of livestock evolved in temperate regions have been introduced into tropical area with high rainfall, humidity and temperatures. Homeotherms are a group of animals which maintain their deep body temperature essentially constant. All the domestic animals are homeotherms. In the case of an inert body, basic thermodynamic forces establishes an equilibrium in which the body attains the same temperature of the surrounding environment. The same law applies to homeothermic animals also. Therefore, these animals will have to make compensatory physiological and behavioural adjustments to keep a constant deep-body temperature. While digestion of food takes place in the body of animals, a portion of the energy in the feed is converted into heat. This metabolic heat plus the heat gained from the environment through conduction, convection and radiation results in excess heat gain to the animal, which has to be dissipated, if heat balance is to be maintained. For this the animal depends on various physiological and behavioural functions. This balancing act by which a constant normal core temperature is maintained is known as homeothermy. Heat production is regulated by hormonal secretions, changes in muscle tone, shivering and by voluntary muscular activity. Heat loss is controlled by vasodialatation, increasing the cutaneous circulation and evaporative loss. The animal reduces its feed intake as well as production, drink more water. In long term the hair coat becomes lighter with less insulation. The animal will also exhibit postural changes and behavioural adjustments. They will try to increase surface area, reduce physical activity and seek shade.

A farm microclimate refers to the specific climatic conditions of a small, localized area within a farm. These conditions can differ significantly from the broader regional climate due to various natural and man-made factors. Understanding and managing microclimates is crucial for optimizing crop growth, animal welfare, and overall farm productivity. Modern commercial dairy production requires a special approach to the microclimate on the farm. High quality milk and animal health depend on the conditions of their keeping. At the same time, farm for dairy production for the most part do not have the means to control and manage the microclimate, in contrast to poultry farm. When organizing the correct process of controlling the microclimate, a prerequisite is the presence of an automated system for collecting data. Generally animals adapt to a wide range of weather conditions although their growth and productivity varies with weather conditions. Buffaloes and cows form the main component in dairy industry. The extent to which these animals can adapt to different weather conditions is given below: Successful management of buffalo rearing will be incomplete without wellplanned and adequate housing facilities (Fig.10.1).
Improper planning in the arrangement of animal housing may result in management problems, increase in disease incidence, additional labour charges and hence decrease in the profit of the farmer. During erection of a house for dairy buffaloes, care should be taken to provide comfortable accommodation for individual animals. It is important to ensure:
• Proper sanitation
• Durability
• Abundant supply of clean water
• Arrangements for the production of clean milk under convenient and
economic conditions.
Buffaloes may be successfully housed under a wide variety of conditions, ranging from close confinement to little restrictions except at milking time. However, two types of farms are in general use.

Change in weather affects growth and development of plants. The extent of these effects depends upon the range or severity of change of weather. It is very much possible to change the weather in relatively small area to reap better harvest. Micro weather modification is defined as, “The manipulation of weather elements at increasing or decreasing the duration, intensity, quality etc., for desired effects at microlevel of crop under investigation”.

The climate near the ground can be managed partly by influencing the moisture status and temperature of the upper soil layers, e.g. by mulching and partly by action above the ground e.g. by shading or use of wind breaks.