Metagenomics and Microbial Ecology

Techniques and Applications

Surajit De Mandal, Amrita Kumari Panda, N. Senthil Kumar, Satpal Singh Bisht, Fengliang Jin, Surajit De Mandal, Amrita Kumari Panda, N. Senthil Kumar, Satpal Singh Bisht, Fengliang Jin

• Publisher: CRC Press
• Year: 2021
• Print ISBN: 9780367487348
• eBook ISBN: 9781000482232
• Edition: 1
• Topic: Biological Sciences
• Subtopic: Biology
• Index: Biological Sciences

Microorganisms comprise the greatest genetic diversity in the natural ecosystem, and characterization of these microbes is an essential step towards discovering novel products or understanding complex biological mechanisms. The advancement of metagenomics coupled with the introduction of high-throughput, cost-effective NGS technology has expanded the possibilities of microbial research in various biological systems. In addition to traditional culture and biochemical characteristics, omics approaches (metagenomics, metaproteomics, and metatranscriptomics) are useful for analyzing complete microbial communities and their functional attributes in various environments.

Metagenomics and Microbial Ecology: Techniques and Applications explores the most recent advances in metagenomics research in the landscape of next-generation sequencing technologies. This book also describes how advances in sequencing technologies are used to study invisible microbes as well as the relationships between microorganisms in their respective environments.

Features:

• Covers a wide range of concepts, investigations, and technological advancement in metagenomics at the global level.
• Highlights the novel and recent approaches to analyze microbial diversity and its functional attributes.
• Features a range of chapters that present an introduction to the field and functional insight into various ecosystems.

Section IV

Metagenomics of Various Ecotypes

6

Earthworm Gut Microbiome

The Uncharted Microbiome

Rashi Miglani*, Nagma Parveen, Satpal Singh Bisht*

Laboratory of Earthworm Biotechnology and Microbial Metagenomics

Department of Zoology, D.S.B Campus, Kumaun University, Nainital

Amrita Kumari Panda

Department of Biotechnology, Sant Gahira Guru University, Ambikapur, Chhattisgarh

Monu Bala

Department of Zoology, P.G. College, Syalde, Almora

Jyoti Upadhyay

School of Health Science, University of Petroleum and Studies, Dehradun

Ankit Kumar

Department of Pharmaceutical Sciences, Kumaun University Bhimtal Campus, Bhimtal

Surajit De Mandal

Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China

DOI: 10.1201/9781003042570-10

CONTENTS

6.1 Introduction

6.2 Microbiome of Earthworm

6.3 Gut Microbiome and Its Beneficial Effect in Earthworms

6.4 The Impact of Earthworm Gut Microbiome on Nutrient Cycling

6.5 Genomics Approaches to Studying Gut Microbiology of Earthworm

6.6 Future Perspectives

6.1 Introduction

Earthworms are nature’s best recyclers, play a significant role in many ecological processes such as the formation of soil structure, and maintain biogeochemical cycling (Gong et al. 2018). As a keystone species, earthworm represents the largest animal biomass of terrestrial ecosystem, up to 90% of soil fauna (Edward 1983; Lavelle and Spain 2001). The earthworm’s gut has massive space and abundant bacterial diversity, which contributes to microbial survival. The earthworm gut contains ~89.5 million liters of soil residue, and within 10 to 40 years, ~50% and ~90% of soil can move through the earthworm gut (Drake and Horn 2007; Pass et al. 2015; Thakuria et al. 2010).

Earthworms have the propensity to consume soil, and the related material—indeed, the composition of soil—is significantly influenced by these voracious feeders. It is essential to understand the physiological, morphological, and behavioral effects of earthworm on soil function (Arrow 1, Figure 6.1). Past studies suggest that soil microbial communities can mediate the impact of earthworms on soil functions (Arrow 2, Figure 6.1) (Medina-Sauza et al. 2019). Hence, different morpho groups, namely epigeic, endogeic, and anecic earthworms, which select soil microorganisms, mainly depend upon different kinds of species and show the effect on the soil microbial community (Byzov et al. 2015).

FIGURE 6.1 Microorganisms are indirectly arbitrated through earthworms’ impact on plant growth and nitrogen cycling. The role of earthworms on nutrient cycling is either direct (1) or indirect (2). Earthworms control the functioning of the ecosystem by changing microbial groups (2a, 2b). The figure indicates both direct and indirect effects are significant in functioning of the ecosystem.

Source: Medina-Sauza et al. (2019)

Earthworm behavior, physiology, and morphology are important to figure out their effect on soil functions (Arrow 1, Figure 6.1). The major purpose of this chapter is to highlight and examine the types of microbial populations that occur in the microbial biome of earthworm gut through metagenomics and to address the future prospective, including the potential impact of gut passage on soil microorganisms and other associated processes like nutrient cycling, change in soil microbiology, and geo-biology of terrestrial habitat.

6.2 Microbiome of Earthworm

The earthworm gut has a movable environment without oxygen to which the microorganisms of soils are subordinated (Drake and Horn 2007). Diversity in microorganisms of ingested soil and cast microorganisms are much influenced by the particular micro-environment of the earthworm gut (Drake et al. 2006). Earthworm nutrition plays a significant role in their effect on soil microbes. The biodiversity and complexity of microorganisms are also influenced by earthworm populations, which may be neutral, negative, or positive. It has been reported in recent research that there is a considerable increase in the population of specific bacterial groups in soils where earthworms are found (Medina-Sauza et al. 2019). Gong et al. (2018) found that in the long term, earthworms, by using their gut micro biota, modify microbes rather than eukaryotes in agriculture fields.

Regardless of the season, nearly 96% of the sequences were assigned only to 50 bacterial populations and three archaeal phyla, mainly constituting Proteobacteria, Acidobacteria, Actinobacteria, Nitrospirae, Bacteroidetes, and Firmicutes (Gong et al. 2018). Bacterial genera with the capacity to cope with high metal contamination were found in the research of Šrut et al. (2019), where they found Dermacoccus, Rhizobium, Symbiobacterium, Rhodobacter, and Rathayibacter to be the five most important bacteria of those that can survive easily in high metal contamination areas inside an earthworm gut. Some of the microbes isolated from various earthworm species are compiled in Table 6.1.

TABLE 6.1 Microbes (Bacteria) Found inside Earthworm Gut

Microbe Name	Family	Function	Reference
Dermacoccus	Dermacoccaceae	Heavy metal resistant (cadmium)	Šrut et al. 2019
Rathayibacter	Microbacteriaceae
Sanguibacter	Sanguibacteraceae
Chryseobacterium	Flavobacteriaceae
Solibacillus	Planococcaceae
Cohnella	Paenibacillaceae	Cellulolytic bacterial
Streptomyces	Streptomycetaceae	Heavy metal resistant (cadmium); glucose isomerase activities	Thakuria et al. 2010; Šrut et al. 2019
Rhizobium	Rhizobiaceae	Bio-fertilizer	Hussain et al. 2016; Šrut et al. 2019
Symbiobacterium	Symbiobacteriaceae	NS
Rhodobacter	Rhodobacteraceae	Perform anoxygenic photosynthesis, degrade insecticide (Acephate)	Drake and Horn 2007; Phugare et al. 2012; Šrut et al. 2019
Paenibacillus sp.	Paenibacillaceae	N2O-producing	Ihssen et al. 2003; Šrut et al. 2019
Protochlamydia/Candidatus	Parachlamydiaceae	Symbionts of earthworms, heavy metal resistant (cadmium)	Nechitaylo et al. 2009; Šrut et al. 2019
Rummeliibacillus	Planococcaceae/Caryophanaceae	NS	Šrut et al. 2019
Shewanella	Shewanellaceae	NS
Pseudomonas sp.	Pseudomonadaceae	NO2-producing	Drake and Horn 2007; Ihssen et al. 2003; Šrut et al. 2019
Roseococcus sp.	Acetobacteraceae	Endosulfan-degrading; chlorinated hydrocarbon-degrading	Šrut et al. 2019; Thakuria et al. 2010; Verma et al. 2006
Patulibacter	Patulibacteraceae	NS	Šrut et al. 2019
Yersinia	Enterobacteriaceae	NS
Parvibaculum	Rhodobiaceae	NS
Agrobacterium	Rhizobiaceae	Heavy metal resistant (cadmium)
Ochrobactrum	Brucellaceae	NS
Thermoactinomyces	Thermoactinomycetaceae	NS
Exiguobacterium	Bacillaceae	Degrade...

Table of contents

• Cover
• Half Title Page
• Title Page
• Copyright Page
• Contents
• Preface
• Editors
• Contributors
• Section I An Overview of Metagenomics
• Section II Metagenomics Tools to Access Microbial Diversity
• Section III Metagenomics of Extreme Environments
• Section IV Metagenomics of Various Ecotypes
• Section V Applications
• Index