Biological soil crusts ecology and management

soil biology as related to land use practices soil biology and biochemistry short communication soil biology and biochemistry abbreviation
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2.3 Soil Biology and Ecology Introduction 85 Lecture 1: Soil Biology and Ecology 87 Demonstration 1: Organic Matter Decomposition in Litter Bags Instructor’s Demonstration Outline 101 Step-by-Step Instructions for Students 103 Demonstration 2: Soil Respiration Instructor’s Demonstration Outline 105 Step-by-Step Instructions for Students 107 Demonstration 3: Assessing Earthworm Populations as Indicators of Soil Quality Instructor’s Demonstration Outline 111 Step-by-Step Instructions for Students 113 Demonstration 4: Soil Arthropods Instructor’s Demonstration Outline 115 Assessment Questions and Key 117 Resources 119 Appendices 1. M ajor Organic Components of Typical Decomposer 121 Food Sources 2. Litter Bag Data Sheet 122 3. Litter Bag Data Sheet Example 123 4. Soil Respiration Data Sheet 124 5. Earthworm Data Sheet 125 6. Arthropod Data Sheet 126 Part 2 – 84 Unit 2.3 Soil Biology & Ecology Introduction: Soil Biology & Ecology UNIT OVERVIEW MODES OF INSTRUCTION LECTURE (1 LECTURE, 1.5 HOURS) This unit introduces students to the The lecture covers the basic biology and ecosystem pro- biological properties and ecosystem cesses of soils, focusing on ways to improve soil quality for processes of agricultural soils. organic farming and gardening systems. DEMONSTRATION 1: ORGANIC MATTER DECOMPOSITION The lecture reviews the constituents of soils (1.5 HOURS) and the physical characteristics and soil ecosystem processes that can be managed to In Demonstration 1, students will learn how to assess the improve soil quality. Demonstrations and capacity of different soils to decompose organic matter. exercises introduce students to techniques Discussion questions ask students to reflect on what envi- used to assess the biological properties of ronmental and management factors might have influenced soils. Such assessments help inform deci- the test results and what the results suggest about nutrient sions about soil management with the goal cycling rates and the quality/health of the soils tested. of maintaining crop productivity and soil DEMONSTRATION 2: SOIL RESPIRATION (1 HOUR) health in organic farming and gardening Demonstration 2 covers the use of Draeger gas detection systems. tubes for measuring carbon dioxide levels liberated from soils as an indicator of soil biological activity and soil qual- ity/health. DEMONSTRATION 3: EARTHWORM POPULATION (1 HOUR) Demonstration 3 takes students through the process of sampling soil for earthworm types. Discussion questions ask students to consider the presence and abundance of certain earthworm types as indicators of soil quality/health. DEMONSTRATION 4: SOIL ARTHROPODS (1 HOUR) Demonstration 4 covers the preparation and materials used to collect and identify soil arthropods. Discussion questions ask students to consider the presence and diversity of soil arthropods as indicators of soil quality/health. ASSESSMENT QUESTIONS (1 HOUR) Assessment questions reinforce key unit concepts and skills. LEARNING OBJECTIVES CONCEPTS ÊUÊ-œˆÊµÕˆÌÞÉ܈Ê…iÌ… ÊUʈ˜iÀˆâ̈œ˜Éˆ““œLˆˆâ̈œ˜Ê ÊUÊÕ̜ÌÀœ«…ˆVɅiÌiÀœÌÀœ«…ˆVÊvœœ`ÊÜiLà ÊUÊ՘V̈œ˜ÊÀœÕ«ÃʜvÊ܈ÊLˆœÌ ÊUÊ,…ˆâœÃ«…iÀiÊiVœœÞ ÊUʘi“i˜ÌÊivviVÌÃʜ˜Ê܈ÊiVœÃÞÃÌi“à Unit 2.3 Part 2 – 85 Introduction Soil Biology & EcologySKILLS ÊUÊœÜÊ̜ÊÃÃiÃÃÊ܈ÃÊvœÀÊLˆœœˆVÊV̈ۈÌÞÊ through measuring the rate of decomposition of cellulose ÊUÊœÜÊ̜ÊÃÃiÃÃÊ܈ÊLˆœœˆVÊV̈ۈÌÞÊ̅ÀœÕ…Ê measuring soil respiration ÊUÊœÜÊ̜ÊÃÃiÃÃÊ܈ÊLˆœœˆVÊV̈ۈÌÞÊ̅ÀœÕ…Ê earthworm census ÊUÊœÜÊ̜ÊÃÃiÃÃÊ̅iÊ܈ÊiVœÃÞÃÌi“ÊÃÌÀÕVÌÕÀiÊ through a soil arthropod census Part 2 – 86 Unit 2.3 Soil Biology & Ecology Introduction Lecture 1: Soil Biology & Ecology Pre-Assessment Questions 1. What is soil? 2. What forms of life exist in soil ecosystems? 3. How would you define a “healthy” agricultural soil? 4. What is a food web? 5. Can you describe a decomposer food web that may exist in the soil? 6. What might be some negative eec ff ts of the long-term practice of monoculture cropping and the use of synthetic chemical fertilizers and pest control agents on the soil ecosystem? A. What Is Soil? (should be a review in part; see also Unit 2.1, Soils and Soil Physical Properties) 1. Soil components a) Mineral i. Derived from parent material b) Soil organic matter c) Water and air i. 1/2 soil volume = pore space ii. Importance of gas diusion: ff When diffusion is slow, as with water-saturated soil, respiration byproducts (such as CO ) accumulate and inhibit aerobic processes (such 2 as respiration itself) iii. CO is about 1% in dry soil, up to 10% in saturated soil 2 d) Biota: The smallest life forms are inseparable from soil organic matter 2. Soil structure vs. soil texture a) Soil texture, a native characteristic i. Soil texture: The relative percentage of sand, silt, and clay particles ii. The bricks, boards, and mortar (the physical materials) that make up soil iii. The particle sizes have surface area:volume eec ff ts. This influences properties such as cation exchange capacity (CEC), pore space, water holding capacity, and aggregate formation. b) Soil structure, a manageable characteristic i. Soil structure: The arrangement of soil particles. The “architecture” of soil—what shapes you build with the “bricks, boards and mortar.” ii. Determines movement of gases and water in soil iii. Creates small habitat spaces iv. Water stability: Aggregates that retain shape when wetted maintain a more stable soil structure v. Influences soil tilth/soil health B. What Is a Healthy Soil? (see also Unit 1.1, Managing Soil Health) 1. Question: Is soil merely a solid medium that holds nutrients for plant growth or does soil serve other functions? 2. Soil health and soil quality are generally synonymous 3. Denition of soil health: fi “Capacity of a soil to function, within land use and ecosystem boundaries, to sustain biological productivity, maintain environmental quality, and promote plant, animal, and human health.” Unit 2.3 Part 2 – 87 Lecture 1: Soil Biology & Ecology Soil Biology & Ecology a) Soil is recognized as an essential component of the biosphere b) Soil is required for significant production of food and ber fi c) Soil contributes to maintaining and enhancing air and water quality d) Soil filters and chemically alters water e) The denition of soil health must be br fi oad enough to encompass the many functions of soil 4. Assessment of soil health a) Analogous to monitoring human health b) Indicators needed to identify problems and to monitor the eec ff ts of management c) Requires a holistic approach d) Should include physical, chemical, and biological attributes of soil e) Indicators must be measurable by as many people as possible, at many dier ff ent skill levels f) Denition and assessmen fi t of soil quality is complicated by the fact that soil is not (typically) directly consumed by animals and humans, unlike air and water g) Basic data set of soil health indicators i. Soil texture ii. Rooting depth iii. Water infiltration iv. Bulk density v. Water holding capacity vi. Soil organic matter vii. pH viii. Cation exchange capacity (CEC) ix. Extractable N, P, and K x. Microbial biomass C and N xi. Potentially mineralizable N xii. Soil respiration xiii. Soil temperature 5. Protection of soil health as a national priority a) National Research Council recommendation (1993): “Protecting soil quality, like protecting air and water quality, should be a fundamental goal of national environmental policy” b) National Resource Conservation Service (2012): Healthy soils initiative called “Unlock the Secrets of the Soil” ( c) USDA Sustainable Agriculture Research and Education program (2014): Organized National Conference on Soil Health and Cover Crops ( Conference-on-Cover-Crops-and-Soil-Health) C. Nutrient Cycling and Decomposition 1. Mineralization/immobilization a) Soil nutrients occur as parts of: i. Inorganic compounds: Some of these are available to plants ii. Organic compounds: Are part of living organisms and decaying organic matter. These nutrients are stored (“immobilized”) in the biomass of the organisms and are unavailable until released during decay or consumption. b) Soil organisms are constantly transforming nutrients between these 2 forms Part 2 – 88 Unit 2.3 Soil Biology & Ecology Lecture 1: Soil Biology & Ecology c) Mineralization: Soil organisms excrete inorganic waste compounds that may adhere to CEC sites and/or dissolve in soil water (soil solution) for possible uptake by crop plants. Net mineralization must be greater than net immobilization for nutrients to be available to crop plants. d) Immobilization: Soil organisms consume inorganic compounds to construct living tissues. These nutrients are temporarily stored and unavailable for plant uptake. 2. Soil organic matter (SOM): Includes all organic substances in or on the soil a) Living organisms—include plant roots and all soil biota ( 5% of SOM) i. Cellulose, the major carbohydrate structural building block for plants, is the most abundant compound on earth and the major component of soil organic matter ii. Lignin is the second largest input into SOM b) Fresh and decomposing organic residues (40–60% of SOM) i. Easily decomposable (active, labile) fraction: The quantity of this fraction of SOM changes quickly in response to management practices and is the organic matter fraction from which the majority of plant nutrients are liberated into the soil solution for uptake by plants ii. Moderately decomposable fraction: This fraction is physically and/or chemically more complex than labile OM. Its decomposition is slower and therefore fewer nutrients are mineralized from it in a given season. c) Resistant (recalcitrant) fraction: Also called humus, and is resistant to further decomposition (33–50% of SOM). Has greater inuenc fl e on the structure/physical properties of soils than on nutrient availability. d) See Appendix 1, Major Organic Components of Typical Decomposer Food Sources e) Physical factors influencing decomposition i. Particle size: High surface area:volume = more rapid decomposition. For example, ail fl mowing breaks cover crops into smaller pieces for more rapid decomposition prior to planting a subsequent crop. ii. Some surface properties of plants (e.g., waxes, pubescence) decrease the rate of decomposition iii. High content of structural compounds, e.g., lignin that supports woody plant stems, decreases the rate of decomposition f) Limiting factors in decomposition of SOM i. Nutrient availability: Decomposers tend to concentrate the nutrients that are in short supply, e.g., N, P, and K. Micronutrients are not usually a limiting factor. ii. C:N ratio of organic matter: High abundance of C compared to N slows the decomposition process. If C:N 20–30:1 = net mineralization. If C:N 20–30:1 = net immobilization iii. Soil moisture: Necessary for respiration by organisms doing the decomposition iv. Oxygen levels: Also necessary for respiration by decomposers g) Plant secondary compounds may inhibit decomposition (such as polyphenols, tannins found in many woody perennials) 3. Nitrogen cycle (see t F igure 2.10 in Unit 2.2, Soil Chemistry and Fertility) a) Proteins break down — amino acids — ammonium (form of N usable by some plants) — nitrate (form of N usable by most plants) b) Ammonica fi tion (aerobic or anaerobic): The biochemical process in the N cycle above whereby ammonium is released from nitrogen-containing organic compounds (amino acids) Unit 2.3 Part 2 – 89 Lecture 1: Soil Biology & Ecology Soil Biology & Ecology c) Nitrica fi tion (aerobic): The biochemical process in the N cycle above whereby bacteria convert ammonium to nitrate i. Inhibited by low oxygen or low temperatures ii. This leads to ammonium build-up in cold, wet soils D. Soil Food Webs 1. Soil food web ecology a) Food webs trace the path of energy or nutrients passing from one organism to the next 2. Heterotrophs vs. autotrophs in food webs a) Autotrophs form the base of food webs, and acquire their own C from the atmosphere. In the soil food web, this begins with C fixation by plants, which is photosynthesis. Energy for most life is derived from sunlight that has been transformed by photosynthetic plants into organic compounds. b) Heterotrophs in food webs consume organic matter to acquire carbohydrates for respiration. By consuming organic matter, they release nutrients, making them available to other plants and animals, or become food themselves for other organisms. c) Energy loss = 80–90% at each step in the food chain d) Food web structure and properties i. Resilience = speed of recovery after disturbance. Resilience decreases with increasing number of trophic levels due to increasing complexity—it takes longer to reestablish complex food web relationships ii. Disturbance selects for shorter food chains: In farmed soils, disturbance can be chemical (pesticides, fertilizers) or physical (cultivation, organic matter incorporation, removal of surface organic layer) The frequency of soil disturbance by physical or chemical agricultural inputs and other disturbances is important to the overall assemblage of soil biota and food chain length iii. Fungi:bacteria biomass ratio characteristics of soil ecosystems tPEVDFSUJW1BMSJDVMUVSBHTPJMTFWIBBUJPBSPGPSMFTT IJHIFSJOOPUJMM IFTF5FBS bacterial-dominated food webs with rapid cycling of nutrients. t%FDJEVPVTFTUPSG TPJMT GVOHBMFE UEPNJOB tPVTFSPOJGFTUPSG TPJMT GVOHBMFE UEPNJOB e) Some heterotrophic roles in soil food webs i. Shredders: Shred organic matter, increasing the surface area and making the food available to more microorganisms. These include earthworms and arthropods. ii. Grazers: Feed on bacteria and fungi, stimulating and controlling the growth of those populations. Grazers include protozoa, nematodes, and microarthropods. iii. Higher-level predators: Consume other heterotrophs, like grazers and shredders, helping control the lower trophic-level predator populations f) Unique food web for each ecosystem, determined by: i. Climate ii. Soil/parent material iii. Vegetation iv. Land management practices Part 2 – 90 Unit 2.3 Soil Biology & Ecology Lecture 1: Soil Biology & Ecology UP UPE. Soil Biota 1. Community characteristics a) High diversity of organisms in soil can rival that of coral reef ecosystems b) High abundance of organisms, on the order of hundreds of millions to billions of microbes in 1 g of soil c) High biomass of organisms, e.g., from hundreds to thousands of pounds of microbes per acre of soil 2. Habitats a) Habitats within soil ecosystems are unevenly distributed b) Habitats are concentrated at organic matter sites i. Root zone (rhizosphere) tFTTJPOD4VDPGHBOJTNTPSBTPPUSP t4PNFPPUSFTUYVEBF NPMFDVMFTFMFBTFESPUJOUIFTPJMUIF PPUTSJODMVEJOH sugars and amino acids) may stimulate microorganisms and thus increase labile SOM ii. Litter (dead organic matter on the soil surface) iii. Surfaces of soil aggregates iv. Incorporated organic matter 3. Functional classica fi tion a) Microorganisms i. Colonial growth forms (cells about 1/25,000 inch wide) tBDFSJB UDIBFB BSBOEFBTUZ tFEEBQU"IJHITVSFGBDPMVNFFBWBSUTPONFOWJSFO tFPMPOJTVS FTGBD FTFWJDDSFTQPS tFBTQPPO5PGTPJMUBJOTPODNJMMJPOCJMMJPOCBDFSJBU tJPNBTTUBMFOFRVJWQFSFBDS tVODUJPOBM'PMFTSJODMVEF/ FSTöY OJUSJöFST EFOJUSJöFSTPNQPTFSTEFD UIF byproducts of which help in the formation of soil aggregates), pathogens ii. Mycelial growth forms (hyphae length ranges from a few cells to many yards) tJVOH' FTFUDZBDUJOPNBOEFTFUDZPPN tFUBFOFUS1HBOJDPSFSUUNB tFUBOTMPDBS5OVUSUTJFO tVODUJPOTBM'PMFTSJODMVEF PNQPTFST%FD NVUVBMJTUT UIPHFOTQBPSTUFEBQS H F nematode-trapping fungi) iii. Algae tFE%UPNJOBwiCMVFFFOSHBMHBFZUB BOPQIZ BOEFVLBSPUJDZBMHBF tUFTFOS1FXIFSUTVOMJHIJTBJMBCMFWBOFBSTPJMTVS FGBDBDFUJWXIFOFUIFSJTFNPJTUVS available, too t)FMQCJOETPJMQBSUJDMFT PHFUIFSUFEVDJOHSPTJPOFSUJBMFOQPUJDBM CJPMPHTPJMDSVTUT tFBTFODSFSUBXUJPOFOFUSDBQBDJUZPGTPJMPVHIUISFTUYVEBF t0GFOU QFSHPGTPJM tVODUJPOBM'PMFTSSJNBS1ZFSTPEVDQSFST UIFTJPTZO QIPU/FSTöY b) Microfauna Note: This section and the macrofauna section below are based on information from the European Atlas of Soil Biodiversity; see Resources for details i. Protozoans (1/5000 inch to 1/50 inch wide) Unit 2.3 Part 2 – 91 Lecture 1: Soil Biology & Ecology Soil Biology & Ecology UP CZ DPXTUP UP UP CZ HSXTt4NBMMBOJNBMTFMMVMBS BDMJWJOHJOFSUBXöMNT t&ODUTUNFOZUJOH IJCFSOBJOBDTU Z%JTUJODFUJWFTQPOTFSESZJOHPVU tOIBCJUPSBOTJUUSZ UTPONFOWJSFOTPFPEVDFQSSBQJEMZS – Colpoda divide once or twice per day at 12oC tBMFS4FWEJTUJODUUZQFT – Ciliates have fringe of small hairs used for locomotion – Amoebae have an amorphous body shape – Flagellates have a whip-like tail for locomotion tVODUJPOBM'PMFTSPSTUFEBS1 H FPGCBDFSJB UPUIFSHBOJTNT PPSNJDSPNQPTFSTEFD (feed on detritus) ii. Nematodes (1/500 inch in diameter, 1/20 inch in length) t(MPCBMEJTUSJCVUJPO 2 t4PJMFBCVOEBODNJMMJPON tFS0VUDVUJDMFFDPUUTQSUFTJTUBOSYJOTPU tVODUJPOBM'PMFTSJODMVEF FTPS.PCJWJDS FTPSPNOJW PSTUFEBQSTPNFFTBTJUQBS  tUCVOEBO"FTTJUXJUIIJHI0.UJPOBUSFOPODD iii. Rotifers (1/50 to 1/120 inch long) t FMMVMBS.VMUJDUIPVHITUJMMPQJDPTDNJDS tF-JWJOFSUBXöMNTPONPJTUTPJMTPOFPGNPTUUBCVOEBOUBYBJOUIFPQUFSZMBPGTPJM 2 or litter (32,000 to 2 million per m ) tBOHPVOEFSPCJPTJTESZBOI TVSFWJWESZJOHXOEPPSNJOHGBDTU Z tSJNBS1ZFFEJOHGJFTFHUBTUSBJOH(SUIFCBDFSJBMUöMNPO40.PSPUIFSQBSUJDMFTPS filter feeding on bacteria, yeast, and algae in the soil water tVODUJPOBM'PMFTSFTPS)FSCJW H FPOBMHBF PNQPTFSTEFDFFE GPOEFUSJUVT iv. Tardigrades (1/25 inch) t FMMVMBS.VMUJDUIPVHITUJMMPQJDPTDNJDS tFTUSJBMFSS5BEFTSEJHUBSFMJWPONPTTPSMJDIFO tBOHPVOEFSPCJPTJTESZZIBO TVSFWJWESZJOHXOEPPSNJOHGBUVO tSJNBS1ZFFEJOHGJFTFHUBTUS4PNFVTFTUZMFUTFDQJFS NPTT BMHBF PBOTPPUQS rotifers or nematodes and suck out fluids; others consume whole microfauna tVODUJPOBM'PMFTS FTPS)FSCJWPSTUFEBQS v. Functional roles of microfauna do not include shredding of organic matter into smaller pieces c) Mesofauna i. Potworms (Enchytraeida, 1/50 to 2 inches long) t4NBMMBOOFMJETFEUFMB SFBSPSNTXUI tFUBPMFS5Q) 2 tIPVTBOETN5 in high organic matter soil t/PTXPCVSS tFFE'POGVOHBM ZQIBFI HBOJTNTPPSNJDSFTFDG ii. Collembolans (springtails, 1/100 to 4 inches long) t4NBMMBSPQPETUISFEUFMB SJOTFDUT XJUI FTNJUUIFNPTUPVTOVNFSTPJM arthropods tF-JWJOTPJMBOEMFBGFSMJUU tFET)VOESUIPVTBOETQFSIBOEGVMPGTPJMIJHIJO40. tFFE'POGVOHBM ZQIBFICBDFSJB UEFUSJUVT Part 2 – 92 Unit 2.3 Soil Biology & Ecology Lecture 1: Soil Biology & Ecology UP UP UP UP CZ CZ BU UP UP iii. Mites (acari, 1/125 to 1/30 inches long) t4NBMMBDIOJETBSFEUFMB STQJEFST XJUI PMMFNCPMBOTDUIFNPTUPVTOVNFSTPJM arthropods (1000 to 10,000 per m2) t(MPCBMEJTUSJCVUJPO tF-JWJOTPJMBOEJOUTIBCJUBXJUIIJHIUJUJFTRVBOPG0. tSJNBSJMZ1 PSTUFEBQSFFEJOHGPOPMMFNCPMB D PEFTUOFNBJOTFDUMBSBFW iv. Insect larvae tMZ'B FS %JQUMBSBFWFBSPCBCMZQSUIFNPTUJNQPSUUBO tOIPNFPNQPTUD FNTTUTZCMBDLTPMEJFSøZMBSBFW JOUIFGBNJMZ ZJEBFUJPNBUS4 order Diptera) can play a key role in consuming organic matter, on par with earthworms tFSTF%JWGVODUJPOBMPMFTSJODMVEF PSTUFEBS1 FTBTJUQBS FTPSIFSCJWPNQPTFSTEFD (feeding on detritus) v. Symphyla (1/125 to 1/30 inches) t4NBMMTPJMFMMJOHEX ZSJBQPETNFEUFMBSNJMMJQFEFTBOEUJQFEFTFOD tSJNBSJMZ1UFBZJOHEFDBUJPOFHFUBWBOE HBOJTNTPPSNJDSCVUBMTP TFFET PPUTSBOE root hairs in agroecosystems, thus damaging crops when they do t6Q QFSN vi. Overall, mesofauna regulate microfauna (and other mesofauna) by grazing vii. Minor shredding of organic matter viii. Total of 500 to 200,000 per square meter, far less abundant and with lower biomass than microfauna d) Macrofauna i. Earthworms (1/3 to 45 inches long) tJDBMPMPHFDUZQFT HFOFDJD"‰MBSFMJWJOUQFSNBOFOTXPCVSSJOUIF TPJMFFEG on litter from the surface mixed with ingested soil; endogeic—small, live in temporary burrows in the soil, feed on rich soils to obtain nutrients from organic matter; epigeic—small, live at the soil surface in litter, feed on litter there t0CUBJOOVUSJUJPOPNGSQBSUJBMMZPNQPTFEEFDHBOJDPSFSUUNBBOEQBSUPNGS microbes living on the organic residues they ingest tFUUJNVMB4PCJBMNJDSBDUJWJUZPVHIUISFDFòUTPO40. PCJBMNJDSUJPOJOPDVMBPUPO substrates, soil structure, etc. t.JYBOEFUFHBSBHHTPJM tFBTFODSFSUBXUJPOBJOöMUS tWJEFPS1DIBOOFMTPSGPPUSUJPOBQFOFUSEFFQPUJOTPJM tVSZBOEFETISHBOJDPSFSUUNB tFCVOEBOD"FBTFTEFDSBGFSUFEJTUVSCBOD UJMMBHFDIFNJDBMT ii. Myriapods t.JMMJQFEFT %JQMPQPEB JODIFTMPOH BOEUJQFEFTFODIJMPQPEB  11 inches long) t.JMMJQFEFTFMJWJOFSMJUUBOEVQQFSFSTZMBPGTPJMTPNFFBSFEEFSTTISUUIBFFEGPO organic matter, others are predators on arthropods or earthworms, others pierce and suck plant cells. More common in soils high in calcium carbonate (e.g., from 2 limestone); 15 to 800 per m . tHF-BSTQFDJFTPGUJQFEFTFODFMJWJOFSMJUUPSDMPTFUIFTPJMTVS FGBDXIJMFTNBMM and narrow species of centipedes live in deeper soil layers. They are primarily generalist predators consuming insect adults and larvae, collembolans, mites, 2 nematodes, potworms and earthworms, and occasionally leaf litter; 20-300 per m . Unit 2.3 Part 2 – 93 Lecture 1: Soil Biology & Ecology Soil Biology & Ecology UP UPUP UP UP UP iii. Isopods (woodlice, 1/15 to 2 inches long) t FBOTSVTUBDFEUFMBSFSTMPCTUBOEBCTDS tF-JWJOMFBG FSMJUUJOUJPO FHFUBWVOEFSPOFTTU t(BMMZFOFSFBS PNQPTFSTEFDFFEJOHGPOEFBEHBOJDPS FSJBMUNBCVUTPNFUJNFTFBS predators of bacteria, fungivores, or herbivores iv. Mollusks (snails and slugs, ¼ inch to 10 inches) tF-JWJOEBNQTPJMPOEJUJPOTD BMUIPVHITOBJMTDBOFIJCFSUOBPSGVQFBSTZJOESZ conditions) t.PTUBDFUJWUOJHIPSPO DMPVEZPHHZGTZEB t4NBMMUPNQPOFODPGTPJMGBVOBCJPNBTTCVUDBOCFPGIJHIPOPNJDSBHBOE ecological signicanc fi e (especially when populations near ½ million per acre) tSJNBSJMZ1 FTPSIFSCJWFTQFDJBMMZPGUDVMFOTVDPMJBHFGTVDIBTTFFEMJOHTBOEGSVJU near the ground, but also detritivores v. Insects tZ.BOJOTFDUTFMJWJOPSPOUIFTPJMBTMBSBFWPS BEVMUTBOEUIVTöMMZNBOGVODUJPOBM roles in the soil food web. Two examples include: – Ants: Ant diversity can be very high, with tens to hundreds of species in a few acres. Ants fulfill multiple trophic roles, e.g., herbivores, predators, scavengers, parasites. – Carabid beetles: Both larvae and adults may live in the soil. May be predators, e.g., feeding on snails or collembola, fungivores, frugivores (eating seeds), or herbivores. vi. Macrofauna shred and incorporate plant remains (may become pests by feeding on living plants if insucien ffi t organic residues present) vii. Also alter the soil structure, e.g., by burrowing, mixing, defecating, and helping form soil aggregates e) Megafauna i. Large invertebrates, vertebrates, including moles, mice, rabbits, gophers, snakes, and lizards ii. Primary ecosystem engineers of the soil: Important for moving and turning soil, contributing to nutrient cycling, aeration, and drainage iii. Fill a range of functional roles: Herbivores and predators of invertebrates and small vertebrates F. Rhizosphere Ecology 1. Definitions a) Rhizosphere (R): The narrow zone of soil subject to the influence of living roots, as manifested by the leakage or exudation of substances that promote or inhibit microbial activity b) Rhizoplane (r): The actual root surface, which provides a highly favorable nutrient base for many species of bacteria, archaea and fungi c) Edaphosphere (S): Soil beyond root inuenc fl e d) Rhizosphere Eec ff t: Soil microorganisms are stimulated by the roots i. R:S ratio generally greater than 1 (i.e., more biota in R than in S) e) Rhizosphere succession: The sequence of changes in the composition and densities of soil microbes and fauna in the area surrounding a growing root (see below) Part 2 – 94 Unit 2.3 Soil Biology & Ecology Lecture 1: Soil Biology & Ecology BU UP UP 2. Roots a) Root environment i. Determined by above-ground processes (products of photosynthesis are translocated to roots) ii. Exudates (see below), sloughed hairs, and epidermal (root’s surface) cells feed soil organisms in R and r iii. Plant roots also can release bicarbonate (HCO -), which raises the soil pH. This can 3 +3 +2 +2 +1 make some cations (e.g., Fe , Ca , Mg , and K ) unavailable to plants. Irrigation water may also contain bicarbonate and aec ff t soil p H and availability of some nutrients. iv. Oxygen decreases, CO increases in root zone over time due to plant and R organism 2 respiration b) Root form i. Fibrous roots t.PTUPUTNPOPD H F BTTFTSHPSO D tSJNBS1ZPPUSFEFQMBDSTFSJFTPGUJUJPVTFOBEWPPUTS ii. Tap roots t.PTUPUTNPOPDBOEHZNOPTQFSNT tBQ5PPUSQFSTJTUTBOEPSNTGZNBOBMFSUMBBODIFTCS iii. Root depth t4QFDJFT TQFDJöDFEJOøVFODUBMPONFOWJSFOPOEJUJPOTD c) Root structure i. Root cap tF-JWFMMTDFEPEVDQSFNNFSJTU tFDPUUTS1 PPUSMJLFBCVETDBMF tUMZPOTUBOFEFQMBDS oZEBUVSOFS WP t3FTQPOETWJUBZSH ii. Meristematic zone: 2 mm (.08 inch) zone where most cell division happens iii. Zone of elongation: Rapid growth, cells from meristem iv. Mucilage tFSTWPPPUSPNGSUJQJOOJOHCFHPGPPUSIBJSPOF tFEFU4FDSPPUSDBQBOEFQJEFSNBMFMMTD tPTTJCMF1GVODUJPOTFTVCSUJDB-BOEFDPUUTQSPPUSBTJUPPVHIUISUIF TPJMIFMQT with nutrient uptake, prevents drying, lls spac fi es between root and soil and helps bind soil aggregates, food for microbes, including benecial micr fi obes v. Root hair (dier ff entiation) zone tFS"BMFSUMBXUITPSHPVUPGTJOHMFFQJEFSNBMFMMTDPQJDPTDNJDS t3PPUIBJSTFWIBFMJGTQBOPGTZEBFFLTX SZFUTQMBODBOFPEVDQSFSWPNJMMJPO per day t%POPUPNFCFDHFMBSTUSVDBMUVS PPUTSUIPVHIIFMQBODIPSUIFUQMBOJOUIFTPJM t,FZPMFSJTWJOHPJNQSUOVUSJFOBCTPSQUJPOFBTJOHJODSTVSFGBDFBBSPSGUOVUSJFO and water uptake. Root hairs make up the majority of root surface area. tPPE'FTDTPVSUUIBTVQQPSUFPTQIFSSIJ PCFTNJDSFUSPOJCVUDUOJöDBOTJHUTBNPVO of soil organic matter vi. Lateral roots tFUJOB0SJHPNGSUIFBTDVMBSWCVOEMFJOTJEFUIFPPUSPSDYFU tPSYFUBOEFQJEFSNJTFBSFESVQUVSOFXBMFSUMBPPUS tBDFSJBUFPMPOJDUIFTFFHFODFNFSFTTJU Unit 2.3 Part 2 – 95 Lecture 1: Soil Biology & Ecology Soil Biology & Ecology CZ CZ UP HSXT CZ UP UP CZ CZ CZ vii. Vascular bundle tZMFN9BOEQIMPFNJOUIFPPUSPSDYFU tPOOFDUTPPUTSUIFFTUSPGUIF UQMBOJODMVEJOHPSGBOTQPSUSUPGUIFUJDPTZOQIPU products (sugars) to the roots and of water and nutrients from the soil up to the aboveground portion of the plant tPMJBS'TZBTQSZNBFWNPPUJOPPUTS EFQFOETPONPMFDVMBSU FJHIX t )FSCJDJEFTUJCJPUJDTBOZNBBMTPFWNPPUJOPPUTS tDJOZPNFQUUS4FEWNPPNGSPMFVTFTWMFBPPUTSJOISTCBDFSJBUJOUIF rhizosphere were suppressed by the streptomycin d) Root nutrition i. Maximum nutrient uptake occurs behind meristem (in the elongation and root hair zones) ii. Water and nutrients are withdrawn from narrow band around roots iii. Replenished from surrounding soil by mass o fl w (the movement of nutrients with the overall o fl w of water to plant roots); all ions in solution move towards root during mass flow iv. If mass o fl w is slower than uptake, a depletion zone is created around the root, resulting in lack of some nutrients v. If uptake is slower than mass flow for a particular ion (or even nonexistent if the ion is not used by the plant) certain ions may accumulate around the root e) Root exudates i. Amounts toFNPSFSTUFOUIFTPJMPNGS FTUYVEBFTMPVHIFE FMMTDBOEPPUSIBJSTUIBO is present as fibrous roots at end of growing season = substantial contribution to SOM tUNPVO"PGFTUYVEBFFBTFEJODS – Wetting, after a drying spell – Physical or chemical injury (e.g., mowing, grazing of perennial grass cover crop) – Abrasion, phytotoxic residues, osmotic stress tUNPVO"PGFUYVEBFBSWJFTXJUIUQMBOTQFDJFTBOE BHFBTFMMXBTUIFTPJMUPONFOWJSFO ii. Types tFTUBESZBSCPIBOEBNJOPBDJETDIFEFTFBS.SPTUUTPNQPOFODPGFTUYVEBF – 10 sugars, glucose and fructose most common – 25 amino acids tMTP"HBOJDPS BDJETUUGBZ BDJET PMTFSTUFO ZNFTUJMFPMBW PNQPVOETDBOEXUIPSH factors tZQF5PGFUYVEBFBSJFTWXJUIUQMBO TQFDJFT BHFTPJMUPONFOWJSFO t%JóDVMUFUBTFQBSUQMBOBOEPCFNJDSFTDTPVS iii. Exudates released from meristem zone tPEFTU/FNBBOEFTPPTQPSFUFHBSPOHDFUIFS f) Management eec ff ts on rhizosphere i. Synthetic fertilizers t4PNFUJNFTOPFDUFò t4PNFUJNFTFBTFJODS R:S indirectly through stimulation of plant growth ii. Organic manures t4BNFFDJOEJSUFQPTJUJWFDUFòPO R:S Part 2 – 96 Unit 2.3 Soil Biology & Ecology Lecture 1: Soil Biology & Ecology UP CZ UP UPtMTP"ZNBFBTFEFDS R:S ratio since edaphic (S) microbes are also stimulated by organic matter input tGFS"UFFLTXPGPNQPTJUJPO EFD R:S generally increases 3. Soil organisms a) Bacteria and archaea i. Most responsive to plant exudates ii. 2 to 20 fold increase in bacterial populations in R vs. S iii. Pseudomonas most consistently abundant in rhizosphere iv. Also Rhizobium (some are used in DNA transfer as part of genetic engineering) and Achromobacter v. Azotobacter, non-symbiotic nitrogen fixer tGFEUJOPDVMBPOTFFEDBOQFSTJTUJOFPTQIFSSIJ vi. Rhizobium, Nitrosomonas, and Nitrobacter, all important to the nitrogen cycle (see t Figure 2.10 in Unit 2.2), common in R b) Fungi i. Average increase of 10 to 20 fold in R of crop plants from S ii. Fusarium is a dominant genera of R fungi iii. Mycorrhizae can provide physical and chemical suppression of pathogens c) Protozoans i. Mainly bacteria grazers, so some increase is expected in R ii. Example: In a wheat eld fi , bacteria R:S was 23:1, protozoan R:S was 2:1 iii. Some large amoebae may provide biocontrol of some fungi d) Nematodes i. Root substances stimulate egg hatching of some parasitic nematodes ii. Host and non-host plants may stimulate hatching of nematodes, e.g., some crucifers and chenopods stimulate Heterodera hatching, but don’t support root invasion by larvae. Some plants will cause eggs of parasitic nematodes to hatch, but then are not susceptible to attack by the parasite. Therefore the plant stays healthy, and the nematodes fail to thrive. iii. Nematodes tend to congregate around elongation zone of roots iv. Degree of nematode attraction is proportional to root growth rate v. Some root exudates repel nematodes (e.g., isothiocyanates in mustard) e) Microarthropods i. Some grazers consistently more abundant around roots f) Rhizosphere succession i. Root tip releases labile carbon ii. Labile carbon stimulates rapid increase of microbes and thus nutrient immobilization in R iii. Grazers increase, tracking the microbe population increases iv. Water and carbon in root hair zone decrease v. Microbes eventually decrease; grazers cause net mineralization and release of nutrients from SOM vi. Later, grazers encyst or migrate Unit 2.3 Part 2 – 97 Lecture 1: Soil Biology & Ecology Soil Biology & EcologyG. Management Eec ff ts on Soil Ecosystems 1. No-tillage or reduced-tillage cropping systems a) Organic litter is retained on the soil surface b) Physical disturbance is minimized c) Surface soil stays cooler and moister d) More surface organic matter available as food substrate e) Ratio of fungi to bacteria increases over time f) Earthworms and arthropods become more plentiful g) Eec ff ts on nutrient cycling: May increase total soil N, improve N use ecienc ffi y of plants, but may increase N O emissions 2 h) Eec ff ts on soil physical properties: May increase SOM and aggregation 2. Rotations a) Monocultures and clean cultivation i. Create little habitat for soil organisms, leading to less abundant and diverse soil ecosystems ii. Consistent plant hosts may serve to develop populations of pathogenic organisms, causing pest problems and crop losses that facilitate the need for pesticide use. b) Complex rotations i. Result in greater variety of microbial food sources (roots, root exudates, and residues) ii. Increase diversity of soil organisms, leading to increased competition for resources, as well as predation of pathogens and pests iii. Interrupt plant-host pest cycles c) Multiculture or polyculture i. Growing more than one crop in one field ii. More closely mimics natural ecosystem iii. Likely to support even greater diversity of soil organisms, especially invertebrates iv. Also interrupts plant-host pest cycles 3. Biocides (insecticides, herbicides, fungicides) a) Eec ff ts vary depending on: i. Type of chemical ii. Species of soil organism in question iii. Concentration and other exposure factors b) High levels of pesticide use generally reduce food web complexity i. Methyl bromide and other fumigants are extreme examples, resulting in temporary soil sterilization ii. Eliminate most organisms iii. Some bacteria quickly return iv. Other organisms only slowly return c) Biocides and predator-release phenomenon i. In cases where biocides selectively eliminate predators, lower trophic levels may become more abundant ii. Destabilizing eec ff t on food webs tBJOHSH0FSWPOPPEGFTDTPVSFTVMUTSJOEFQMFUJPOPGPPEGFTDTPVS tUJPOPQVMB1YQMPTJPO FFEXPMMPGBTIDS Part 2 – 98 Unit 2.3 Soil Biology & Ecology Lecture 1: Soil Biology & Ecology CZtUJPONNPCJMJBPG OVUSUTJFOFEXPMMPGBQJESUJPOBMJBNJOFSBFUUUIBJTOPU necessarily compatible with crop needs. May result in leaching of water-soluble nutrients, especially forms of N. d) Earthworms i. Most strongly aec ff ted (negatively) by fungicides and fumigants ii. Herbicides tU%POTFFNCFFDEJSUMZYJDPUFBSPSNTXUI tFDOEJSUFUJWOFHBFDUFòPVHIUISUJPOFMJNJOBPGUJPOFHFUBW 4. Food web structures a) Fungi/bacteria ratio b) Dominant microbe inuenc fl es other trophic levels 5. Interaction with fertility needs (also see Unit 1.1) a) Measures of available nitrogen i. Conventional cropping systems t.PTU/WJEFEPQSBEEJUJPOTPGFSGFSUJMJ tUTFNFO.FBTVSPGFUBOJUSFøFDSUFMZUBDVSBD CVUIJHIMZBMMZ FNQPSUUXIBJT available to plants t,FZUNBOBHFNFOEFDJTJPOTFBSXIFOBQQMZFSGFSUJMJ ii. Cropping systems based on organic matter management t4PJMPPEGFCXPNFTCFDQSJNBSZFDTPVSPG/FEEFSJWPNGSHBOJDPSFSUUNBJOQVUT t4PJMTJTBOBMZJOUMZFóDJFONBOBHFEGBSNJOHFNTTUTZZNBFUJOEJDBwFUJOBEFRVBi levels of N at any given time because much of soil N is immobilized tFUJWVNVMBFMFBTFSPGBMNJOFS/FSWPXJOHPSHTFBTPOZNBDIUNBUTBNPVOTFFOJO conventional system tJOH.BOBHUIFUJNJOHPGUJPOBMJBNJOFSPVHI UIS UJMMBHF0.RVBMJUZ HF/ UJPBS incorporation of high-OM nutrient amendments, irrigation) by soil food web becomes more critical tGNBOBHFE FMMXMFTTSJTLPGOVUSUJFOMPTTPVHIUISMFBDIJOHPSUJPOUJMJBPMBW Unit 2.3 Part 2 – 99 Lecture 1: Soil Biology & Ecology Soil Biology & Ecology UP CZ UPUP SBBUCZPart 2 – 100 Unit 2.3 Soil Biology & Ecology Demonstration 1: Organic Matter Decomposition in Litter Bags for the instructor OVERVIEW MATERIALS NEEDED ÊUÊ7…Ì“˜ÊwÌiÀÊ««iÀÊ`ˆÃVà To demonstrate the capacity of † ÊUʏÃ̈VʓiÅÊLà different soils to decompose organic ÊUʏÃÊ̜ʓÀŽÊLÕÀˆÊÈÌià matter, this exercise requires you ÊUʏÌÊŜÛi to bury cellulose disks (Whatman ÊUʈÌÌiÀÊ Ê ÌÊ-…iiÌÊ­ÃiiÊ««i˜`ˆÝÊÓ® filter paper) in a variety of locations. ÊUÊi˜VˆÃÊ This should be done at least two †ÊœÀÊ«Ã̈VʓiÅÊLÃÊޜÕʓÞÊÕÃiÊ«œ˜`ʘ`Ê«œœÊ˜iÌ̈˜Ê weeks prior to the class to allow obtained from a local feed and seed supply. It is a 3/8-inch polypropylene mesh. Cut the mesh into 6-inch x 12-inch decomposition to proceed before the pieces, fold in half, then fold the edges over and staple disks are retrieved on the day of the the edges shut. Other sources are the mesh bags that class. To accelerate decomposition, bulbs are sold in, garlic or onion bags, or the mesh bags that imported rice noodles are packed in. The smaller the filter paper disks can be dipped in “iÅÊÈâiÊ̅iÊӏiÀÊ̅iʜÀ˜ˆÃ“ÃÊ̅ÌÊ܈ÊLiÊiÝVÕ`i`Ê a bucket of water with some fish from the bag. This feature can be exploited by comparing emulsion added just before burial. decomposition rates of organic matter buried in bags of `ˆvviÀi˜ÌʓiÅÊÈâiðÊ"À˜ˆVʓÌÌiÀʈ˜ÊLÃÊ܈̅ÊÛiÀÞÊw˜iÊ mesh will be decomposed primarily by microflora and microfauna. Organic matter in larger mesh bags will also be decomposed by larger fauna. PREPARATION Ê£°ÊViʏˆÌÌiÀÊLÃʈ˜Ê܈ÊÌʏiÃÌÊÌܜÊÜiiŽÃÊ«ÀˆœÀÊ̜ÊVÃÃ°Ê ViÊ̅i“ÊÛiÀ̈VÞʈ˜Ê܈Ê˜`ʏÊÌÊ̅iÊÓiÊ`i«Ì…°Ê œÀÊÊ£äÊV“Ê`ˆÃVÊäÊ̜ʣäÊV“ʈÃÊÊVœ˜Ûi˜ˆi˜ÌÊ`i«Ì…°Ê ÊӰʏÊiV…ÊÈÌiʘ`ʓŽiÊʘœÌiʜvÊ̅iÊLÕÀˆÊœV̈œ˜Ã°Ê A minimum of 3 bags should be placed in each …LˆḬ̀ʜÃÈLiʅLˆÌÌÃʈ˜VÕ`iÊÀˆÃi`ÊÀ`i˜ÊLi`ÃÊ VՏ̈ÛÌi`Êwi`ÃÊvœÜÊwi`ÃʜÀV…À`ÃÊVœ“«œÃÌÊ«ˆiÃÊ vermicompost bins, weedy borders, and on the soil ÃÕÀvViÊ­˜œÌÊLÕÀˆi`®° Unit 2.3 Part 2 – 101 Instructor’s Demonstration 1 Outline Soil Biology & EcologyPROCEDURE PREPARATION TIME 1. After two weeks, bring students out to the 1 hour to make 24 bags, 1 hour to bury 24 bags sites and ask them to observe the biotic, ­œÜÊ``ˆÌˆœ˜Ê̈“iÊvœÀÊ̅iÀˆ˜Ê“ÌiÀˆÃ® abiotic, and human management elements of the soil habitat that each bag was in, DEMONSTRATION TIME noting features such as relative soil moisture, 1.5 hours «ÀiÃi˜ViʜÀÊiۈ`i˜ViÊ­i°°ÊLÕÀÀœÜÃʜÀÊ Ì՘˜iÃ®ÊœvʘÞÊ܈ÊœÀ˜ˆÃ“ÃÊÛiiÌ̈ÛiÊ DISCUSSION QUESTIONS cover and shading, and prior cultivation. 1. After retrieving the litter bags, ask students 2. Students or the instructor can unbury the to offer hypotheses about why the disks bags. This should be done very gently, as the decompose more rapidly in some habitats ««iÀʈÃʏˆŽiÞÊ̜ÊLiÊÛiÀÞÊvÀˆi°Ê­vÊ̜œÊÀ«ˆ`Ê than others. decomposition makes this demonstration `ˆvwVՏÌʘʏÌiÀ˜ÌˆÛiʓÌiÀˆÊ̜ÊÕÃiʈÃÊÊÊÓ°Ê7…ÌÊi˜ÛˆÀœ˜“i˜ÌÊvV̜ÀÃʓˆ…ÌʅÛiÊ xäÉxäÊVœÌ̜˜É«œÞiÃÌiÀÊvLÀˆV°Ê Ûi˜ÊˆvÊ̅iÊ influenced the results? cotton is entirely degraded, the polyester ÊΰÊ7…Ìʓ˜i“i˜ÌÊvV̜ÀÃʓˆ…ÌʅÛiÊ matrix will remain intact. Strips would have influenced the results? to be weighed before and after burial to `iÌiÀ“ˆ˜iʓÃÃʏœÃð®Ê 4. Can you see any signs of biological activity œ˜Ê̅iÊ`ˆÃŽÃÊ­i°°Êv՘Ê“ÞViˆÊ܈Ê 3. Gently brush soil from discs. Ask students ˜ˆ“Ãʈ˜ÛiÀÌiLÀÌiÊviViÃÊVœ““ˆ˜Ṏœ˜®¶ to visually estimate the percentage of the disc remaining. You may wish to provide a Êx°Ê7…ÌÊ`œÊ̅iÊÀiÃՏÌÃÊÃÕiÃÌÊLœÕÌʘÕÌÀˆi˜ÌÊ sheet showing examples of visual estimates of cycling rates in the soils tested? «iÀVi˜ÌiÃÊi°°ÊÊ̜ʅi«ÊÃ̘`À`ˆâiÊÀiÃՏÌð 6. Can these observations for cellulose Ê°Ê,iVœÀ`ÊÀiÃՏÌÃʘ`ÊVVՏÌiÊ̅iÊÛiÀiÊ decomposition rates be extrapolated to other percentage of the disc remaining for each types of organic matter? habitat selected. A sample form is provided ÊÇ°Ê7…ÌÊÀiÊ̅iʏˆ“ˆÌ̈œ˜ÃʜvÊ̅ˆÃʓi̅œ`¶ ­ÃiiÊ««i˜`ˆÝÊÓʈÌÌiÀÊ Ê ÌÊ-…iiÌ®ÊvœÀÊ recording data. Appendix 3 provides an iݓ«iʜvÊÊwi`‡œÕÌÊ`ÌÊÅiiÌ° VARIATIONS If possible, pair the litter bag demonstration with other methods of assessing biological activity, such as: ÊUÊ ÀLœ˜Ê`ˆœÝˆ`iÊiۜṎœ˜Ê­ÃiiÊ i“œ˜ÃÌÀ̈œ˜ÊÓÊ -œˆÊ,iëˆÀ̈œ˜® ÊUÊ À̅ܜÀ“Ê`i˜ÃˆÌÞÊ­ÃiiÊ i“œ˜ÃÌÀ̈œ˜ÊÎÊ À̅ܜÀ“Êœ«ÕÌˆœ˜Ã® ÊUÊՏÀi˜/Êv՘˜iÊiÝÌÀV̈œ˜ÃʜvʓˆVÀœÀ̅Àœ«œ`ÃÊ ­ÃiiÊ i“œ˜ÃÌÀ̈œ˜ÊÊ-œˆÊÀ̅Àœ«œ`î ÊUʈVÀœLˆÊLˆœ“ÃÃʓiÃÕÀi“i˜ÌÃʭ̅ˆÃÊi˜iÀÞÊ requires more extensive lab work, but you might check with local agricultural or ecological researchers to see if anyone doing similar work could accommodate a few samples and help ޜÕÀÊÃÌÕ`i˜ÌÃʘÞâiÊ̅iÊÀiÃՏÌî Part 2 – 102 Unit 2.3 Soil Biology & Ecology Instructor’s Demonstration 1 Outline

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