The Hetch Hetchy Railroad

This post has nothing to do with microbiology, but everything with my love for maps. It is about the former Hetch Hetchy Railroad.

Hetch Hetchy reservoir is the main source of drinking water for the city of San Francisco and other parts of the Bay Area. The densely populated SF Bay Area only gets rainfall in the winter months and is dependent on reservoirs in the Sierra Nevada mountains for the collection and storage of rain and melting snow water for the dry summer months.

The Hetch Hetchy area once was a glacier-formed valley of what is now Yosemite National Park, California. It is located in the Northwestern part of the national park, far away from the much more famous Yosemite Valley. Hetch Hetchy Valley was equally beautiful, but it was turned into a reservoir, an artificial lake, in 1923 upon the completion of the O’Shaughnessy Dam.

O’Shaughnessy Dam at Hetch Hetchy reservoir. Photo by Inklein at English Wikipedia, CC BY-SA 3.0,

Here are two photos comparing Hetch Hetchy valley before and after the dam was completed, taken from roughly the same position.

Screen Shot 2019-07-24 at 5.52.04 PM.png

Top: Hetch Hetchy Valley in the early 1900, with the Tuolumne River. Source: Isaiah West Taber – Sierra Club Bulletin, Vol. VI. No. 4, January, 1908, pg. 211 (Wikipedia). Bottom: Hetch Hetchy reservoir, May 2002. Photo by Daniel Mayer. Source: Wikipedia.

As of today, the Hetch Hetchy Project consists of the reservoir, the dam, hydroelectric plants, and a long aqueduct that carries the water to the SF Bay Area through a long series of tunnels, using only gravity.


Hetch Hetchy Project. Source: By Shannon1 using Adobe Illustrator CS5; aqueduct path data from USGS topos, CC BY-SA 4.0,

The story about the Hetch Hetchy Railroad, built in the 1910s and 1920s to bring the construction crews and materials needed to build the dam, hydroelectric plants, and aqueducts is very interesting if you like history and maps. After completion of the dam in 1923, the HHRR was used to carry tourists and mail to the Northern Yosemite area. However, the steep terrain, sharp curves, and heavy snowfall made it very hard and expensive to operate the railroad. During World War II, HHRR rail materials such as steel and wood were used for war operations, and the railroad was finally completely dismantled in 1949.

Hetch Hetchy Railroad Locomotive #2 in the Travel Town Museum in Los Angeles, 2017. Photo by NearEMPTiness,

Friends of us who live near an area where the railroad used to run told us about the success and decline of the railroad, and pointed us towards some sections where you can still see remnants of how the tracks ran. Even though the rails and wooden cross-ties are now all gone, you can still see the flattened track at some sections. Close to the Hetch Hetchy reservoir, the road to access the lake now runs over the railroad track.

Online maps and photos of the Hetch Hetchy Railroad

Hearing about the now-gone railroad got me interested in mapping the complete course of the railroad. I first searched online and found a couple of railroad and other sites that mentioned it.

  • GhostRails and AbandonedRails (very similar sites) both have a rough map of the first part of the route and some discussion on where to see remnants of the railway
  • San Francisco’s Municipal Transportation Agency has a site that remembers how San Franciscans could take the railway up to the Hetch Hetchy reservoir to visit the site where their drinking water came from and see their tax dollars at work.
  • MTB project has a bike route that follows part of the track around Groveland
  • Wikipedia has a page that describes when the railroad was in operation and which locomotives ran over it. It also describes how steep and curvy the track was.
  • has the GPS coordinates of the start of the track, in California’s Central Valley west of the Don Pedro Reservoir, at Hetch Hetchy Junction
  • There is also a Hetch Hetchy Railroad museum in El Portal, west of Yosemite National Park’s entrance on Highway 140
  • Several old maps were also available online, such as this map at Yosemite News. On the map below,  you can see that it split off from the (still-existing) Sierra Railroad.

Map from 1947 displaying the Hetch Hetchy Railroad

More maps and information about the HH Railroad

The information I found online was not enough detailed to know how the HHRR exactly ran. Luckily, our friends lent us their copy of the book Yosemite’s Hetch Hetchy Railroad by Ted Wurm. The author was part of a group of railfans who traveled the railroad around 1937 and took lots of photos. This book has a map of the railroad route, and several descriptions that allowed me to start to map the exact position of the tracks.

Photo of Ted Wurm's book about the Hetch Hetchy Railroad

Yosemite’s Hetch Hetchy Railroad by Ted Wurm

The Groveland Yosemite Gateway Museum also has a small exhibition on the Hetch Hetchy Railroad. It consists of several photos and a topographical map in which a person called Bill Dagg draw the course of the railroad by hand.

Map of the HHRR in the Groveland Museum, hand-drawn by Bill Dagg

Drawing the exact location of the railroad in Google Earth

These two maps by Ted Wurm and Bill Dagg were a lot more detailed than what I could find online. I was very excited to see how much work these two men had put into mapping the railroad.

Since I could not find an electronic version of the railroad’s course online, I decided to make a KML file myself. KML stands for “Keyhole Markup Language“, and is a way to visualize geographic data in – for example – Google Earth. Google Earth is the advanced version of Google Maps and it allows you to add extra layers. An easy way to make a KML file is to draw a line or a polygon on top of the map displayed in Google Earth.

In order to draw the map, I downloaded Google Earth Pro. There is also a Google Earth Web version that runs in Chrome and that can display KML files, but it did not allow me to make one or edit points.

Using Google Earth satellite views and the maps from Ted Wurm’s book and Bill Dagg’s map from the Groveland Museum it was easy to spot some parts of the now-dismantled railroad. In some places, the railroad is now an unpaved or paved road, while in other spots the old foundations are still visible in the landscape.

Google Maps satellite view of the western-most part of the Hetch Hetchy Railroad. The leftmost and rightmost arrows show visible remnants of the track foundations, while the other arrows show parts that now serve as a road.

I was also very excited to find some historical topographical maps on the website of the USGS from around 1947, just before the railroad was removed. These maps are available as KMZ (zipped KML) files, so you can just overlay them in Google Earth. This allowed me to draw the railroad even more precisely.

Historical topographic map from USGS as a KMZ overlay in Google Earth. The red line is my drawing of the railroad.

This was a fun project to do in Google Earth. In some cases, the historic topographical maps were a bit shifted from the current Google map, and in other cases new roads were put over the historic railroad, so I had to make an educated guess where the tracks had been. But in most spots it was easy to see the old tracks from the satellite images.

Download the Hetch Hetchy Railroad

So here it is, a link to the historic Hetch Hetchy Railroad route (KML file) as drawn by me in Google Earth. If you click on the link it will show you the route in Google Maps.

Or, if you want to edit, download the KMZ file to display in Google Earth. Enjoy!

The Hetch Hetchy Railroad, mapped by Elisabeth Bik

One thing that struck me as amazing is how beautiful the incline of the trail is over certain areas. Look at this elevation profile that Google Earth draw over the complete 68-mile route. In several places, the tracks go up or down a nearly perfect 4 degrees. What a great piece of 1920s engineering that was!

Elevation profile of the Hetch Hetchy Railroad, generated by Google Earth.

August 23, 2019

Good morning everyone!

This post is written from lovely NYC, quite a distance from my hometown in Israel. If you’re working on microbial ecology in the city and care for a cup of coffee (on me!) and a rather interesting chat about science, entreprenurship and agriculture- please contact me via or just find me on Linkedin.

Today post will feature highly recommended podcast, a great antimicrobial resistance review paper, Cocaine effect on gut microbiota, some cool bioinformatics tools papers, fascinating animal microbiome studies and more.

Resources and Podcast

I’m a huge fan of the This Week in Microbiology podcast. On their 201 episode the team hosted Prof. Mark Martin (U of Puget Sound) with some great list of papers for 1st year undergrads- but it is a great opportunity to read about general concepts and direction in micrboiology. I truely enjoed both the episode and the recommended papers.

15 Biotech-Themed Online Courses to Try at Home

Antibiotic Resistance

Defining and combating antibiotic resistance from One Health and Global Health perspectives, Sara Hernando-Amado, Nature Microbiology


An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data, Chenhao Li, Microbiome

Analysing complex metagenomic data with MicroWineBar, Franziska Klincke ,bioRxiv

A systematic NGS-based approach for contaminant detection and functional inference, Sung-Joon Park, bioRxiv

Human and Animal microbiome

Cocaine Induces Inflammatory Gut Milieu by Compromising the Mucosal Barrier Integrity and Altering the Gut Microbiota Colonization, Ernest T. Chivero, Scientific Reports

Influence of the microbiota-gut-brain axis on behavior and welfare in farm animals: A review, Narjis Kraimi, Physiology & Behavior

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system, Yaron Krotman, bioRxiv

Non‐random associations of maternally transmitted symbionts in insects: The roles of drift versus biased co‐transmission and selection, Hugo Mathe-Hubert, Molecular Ecology

The microbiome of the Melitaea cinxia butterfly shows marked variation but is only little explained by the traits of the butterfly or its host plant, G. Minard, Environmental Microbiology

Food microbiome

The occurrence of Listeria monocytogenes is associated with built environment microbiota in three tree fruit processing facilities, Xiaoqing Tan, Microbiome

Environmental microbiome

Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome, Pedro J. Cabello-Yeves, Microbiome

Taxonomic and functional characterization of a microbial community from a volcanic englacial ecosystem in Deception Island, Antarctica, Emma Martinez-Alonso, Scientific Reports

January 15, 2019

Highlights today include the organisms in the healthy infant intestinal microbiome that protect against food allergy, an algorithm to predict aging based on the gut microbiome, and how bacteria adapt to life on the International Space Station. Enjoy!

Pregnancy and early life
Healthy infants harbor intestinal bacteria that protect against food allergy – Taylor Feehley – Nature Medicine

Human gut microbiome
Preprint: Human microbiome aging clocks based on deep learning and tandem of permutation feature importance and accumulated local effects – Fedor Galkin – bioRxiv
(Covered in popular press as Your Gut Microbiome Could Actually Reveal Your Age, Study Shows)

Preprint: The virome in adult monozygotic twins with concordant or discordant gut microbiomes – J. Leonardo Moreno-Gallego – bioRxiv

Human nearly-sterile sites
Review: Microbiome–metabolome reveals the contribution of gut–kidney axis on kidney disease – Yuan-Yuan Chen – Journal of Translational Medicine

Animal experiments
Lactobacillus sakei Alleviates High-fat Diet-induced Obesity and Anxiety in Mice by Inducing AMPK Activation and SIRT1 Expression and Inhibiting Gut Microbiota-mediated NF-κB Activation – Hyo-Min Jang – Molecular Nutrition and Food Research

Aqueous raw and ripe Pu-erh tea extracts alleviate obesity and alter cecal microbiota composition and function in diet-induced obese rats – Yun Xia – Applied Microbiology and Biotechnology

Impact of intramammary inoculation of inactivated Lactobacillus rhamnosus and antibiotics on the milk microbiota of water buffalo with subclinical mastitis – Carlotta Catozzi – PLOS One

Plant, root, and soil microbiome
Superior dispersal ability can lead to persistent ecological dominance throughout succession – Primrose J. Boynton – Applied and Environmental Microbiology

Plant growth-promoting rhizobacterium Pseudomonas PS01 induces salt tolerance in Arabidopsis thaliana – Thanh Nguyen Chu – BMC Research Notes

Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range – Dandan Cheng – PeerJ\

Antifungal potential of bacterial rhizosphere isolates associated with three ethno-medicinal plants (poppy, chamomile, and nettle) – Marija Mojicevic – International Microbiology

Analysis of uranium removal capacity of anaerobic granular sludge bacterial communities under different initial pH conditions – Taotao Zeng – Environmental Science and Pollution Research

Water and extremophile microbiomes
An interspecies malate–pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community – Po-Hsiang Wang – The ISME Journal

Bacterial community assembly in a typical estuarine marsh with multiple environmental gradients – Zhiyuan Yao – Applied and Environmental Microbiology

Effects of salinity on microbialite-associated production in Great Salt Lake, Utah – Melody R. Lindsay – Ecology

Preprint: Capturing the Diversity of Subsurface Microbiota – Choice of Carbon Source for Microcosm Enrichment and Isolation of Groundwater Bacteria – Xiaoqin Wu – bioRxiv

Genetic Evidence for Two Carbon Fixation Pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in Symbiotic and Free-Living Bacteria – Maxim Rubin-Blum – mSphere

Generation of 13C-labeled MUC5AC mucin oligosaccharides for stable isotope probing of host-associated microbial communities – Clayton Evert – ACS Infectious Diseases

Transomics data-driven, ensemble kinetic modeling for system-level understanding and engineering of the cyanobacteria central metabolism – Hiroki Nishiguchi – Metabolic Engineering

Built environment/Microbes in Space
Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil – Ryan A. Blaustein – mSystems
(Covered in the popular press as Good news: space bacteria (probably) aren’t evolving to destroy us)

Science, publishing, and career
Preprint: Tracking the popularity and outcomes of all bioRxiv preprints – Richard J. Abdill – bioRxiv

January 11, 2019

General Microbiome

A great-ape view of the gut microbiome.Nishida AH. Nature Reviews Genetics

Relative reduction of biological and phylogenetic diversity of the oral microbiota of diabetes and pre-diabetes patients. Saeb ATM. Microbial Pathogenesis

Dietary modulation of the microbiome as therapy.Bernard NJ. Nature Reviews Rheumatology

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems.Pacheco AR. Nature Communications

Low-moisture food matrices as probiotic carriers. Marcial-Coba MS . FEMS Microbiology Letters

REVIEW: Cross-Domain and Viral Interactions in the Microbiome.Rowan-Nash AD. Microbiology and Molecular Biology Reviews

The respiratory microbiome and susceptibility to influenza virus infection. Lee KH. PLoS One

Food Microbiome

Metagenomic profiles of different types of Italian high-moisture Mozzarella cheese.Marino M. Food Microbiology

Gut Microbiome

Enhancement of the gut barrier integrity by a microbial metabolite through the Nrf2 pathway.Singh R. Nature Communications

Pilot study of probiotic/colostrum supplementation on gut function in children with autism and gastrointestinal symptoms.Sanctuary MR. PLoS One

Nonsteroidal Anti-inflammatory Drugs Alter the Microbiota and Exacerbate <i>Clostridium difficile</i> Colitis while Dysregulating the Inflammatory Response.Maseda D. mBio


OTUX: V-region specific OTU database for improved 16S rRNA OTU picking and efficient cross-study taxonomic comparison of microbiomes. Yadav D. DNA Research

Streamlining standard bacteriophage methods for higher throughput.Kauffman KM. MethodsX

Indirect DNA extraction method suitable for acidic soil with high clay content. Högfors-Rönnholm E. MethodsX

DATABASE: The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection.Rigden DJ. Nucleic Acid Research

Animal Experiments and Microbiome

Effect of the Nursing Mother on the Gut Microbiome of the Offspring During Early Mouse Development.Treichel NS. Microbial Ecology

Delayed differentiation of vaginal and uterine microbiomes in dairy cows developing postpartum endometritis.Miranda-CasoLuengo R. PLoS One.

Seabird and pinniped shape soil bacterial communities of their settlements in Cape Shirreff, Antarctica.Ramírez-Fernández L. PLoS One

Use of 16S rRNA gene sequencing for prediction of new opportunistic pathogens in chicken ileal and cecal microbiota.Kollarcikova M. Poultry Science

Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle.Delgado B. Scientific  Reports


Marine and Inland Waters

Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Sousa AGG. Microbial Ecology

Stratification, nitrogen fixation, and cyanobacterial bloom stage regulate the planktonic food web structure.Loick-Wilde N. Global Change Biology

Analysis of viral and bacterial communities in groundwater associated with contaminated land.Costeira R. Science of the Total Environment

Plant, Soil, and Air Microbiome

The known and the unknown in soil microbial ecology. Baldrian P. FEMS Microbiology Ecology.

Genomic analysis of bacteria in the Acute Oak Decline pathobiome.Doonan J. Microbial Genomics.

Glutathione S-Transferase Enzymes in Plant-Pathogen Interactions.Gullner G. Frontiers in Plant Science

A comparative metagenomic and spectroscopic analysis of soils from an international point of entry between the US and Mexico.  Cota-Ruiz K. Environmental International

Metagenome tracking biogeographic agroecology: Phytobiota of tomatoes from Virginia, Maryland, North Carolina and California. Ottesen A. Food Microbiology

Temporal Dynamics of Bacterial Communities in Soil and Leachate Water After Swine Manure Application.Rieke EL. Frontiers of Microbiology

September 17, 2018

In today’s Microbiome Digest, look for rhizobacteria that affect plant size, methanogenesis in salt marsh sediments, a murine model for periodontitis, and an exciting preprint that identifies a microbiome in dinosaur bones! Plus, as bonus non-microbiology topics, we consider authorship norms across different disciplines and how forensics might work on Mars.

General Microbiome
(preprint) Life Inside A Dinosaur Bone: A Thriving Microbiome – Evan Thomas Saitta – bioRxiv

Metabolic Interactions of a Chain Elongation Microbiome – Wenhao Han – Applied and Environmental Microbiology

Human Gut Microbiome
Passing the “Acid Test”: Do Proton Pump Inhibitors Affect the Composition of the Microbiome? – Tien Dong – Digestive Diseases and Sciences

The gastric mucosal-associated microbiome in patients with gastric polyposis – Rongrong Ren – Scientific Reports

Animal Experiments
An experimental murine model to study periodontitis – Julie Marchesan – Nature Protocols

The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice – Alida Kindt – Nature Communications

Animal Microbiome
Global Networks of Symbiodinium-Bacteria Within the Coral Holobiont – Rachele Bernasconi – Microbial Ecology

(preprint) Gut microbial compositions mirror caste-specific diets in a major lineage of eusocial insects – Saria Otani -bioRxiv

Plant, Root, and Soil Microbiome
Plant growth-promoting rhizobacteria promote plant size inequality – Alan C. Gange – Scientific Reports

Diversity of active viral infections within the Sphagnum microbiome – Joshua MA Stough – Applied and Environmental Microbiology

The impact of high throughput sequencing on plant health diagnosticsThe impact of high throughput sequencing on plant health diagnostics – Ian Adams -European Journal of Plant Pathology

Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment – Eleanor Jameson – ISME Journal

Water and Extremophile Microbiome
Living at the frontiers of life: extremophiles in Chile and their potential for bioremediation – Roberto Orellana – Frontiers in Microbiology

Spatial structuring of bacterial communities in epilithic biofilms in the Acquarossa river (Italy) – Carolina Chiellini – FEMS Microbial Ecology

A small‐sample kernel association test for correlated data with application to microbiome association studies – Xiang Zhan – Genetic Epidemiology

Science, Publishing, and Career
Thousands of scientists publish a paper every five days – John P. A. Ioannidis – Nature

Alyson’s Non-Microbiology Picks
Sensing with tools extends somatosensory processing beyond the body – Luke E. Miller- Nature

How Will Police Solve Murders on Mars? – Geoff Manaugh – The Atlantic

Lab photo stock fun: Pipetting Sideways

The Verge had a fun article by Rachel Becker on Thursday about funny science stock photos called “Stock photos of scientists reveal that science is mostly about staring – 
Sometimes at chickens“.

In case you did not know, I made a whole collection of these on this blog – brought together on this page: Lab Stock Photo Fails.

And it made me realize that it was time for a new installment of this series. Today, let’s focus on some great ways to pipet sideways. Because gravity is so over-rated.




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January 14, 2018

Today’s digest features brilliant ‘Letters to the Editors’ articles in response to recently published works, and concise microbiome reviews. Lastly, an improved method for assembly of functional metagenomes.

Gut Microbiome

Letters to the Editor: Navigating the Microbiota Seas: Triangulation Finds a Way Forward. Rosen, CE. Cell Host & Microbe.

Perturbations of the gut microbiome genes in infants with atopic dermatitis according to feeding type. Lee, M-J. Journal of Allergy and Clinical Immunology

Insect Microbiome

REVIEW: Functional roles and metabolic niches in the honey bee gut microbiota. Bonilla-Rosso, G. Current Opinion in Microbiology

Letters to the Editor: Insect Gut Microbiota: Accessories to the Bite. Aksoy, S. Cell Host & Microbe

Animal Experiments and Microbiome

Characterisation of the intestinal microbial communities of rainbow trout (Oncorhynchus mykiss) fed with Hermetia illucens (black soldier fly) partially defatted larva meal as partial dietary protein source. Bruni, L. Aquaculture

REVIEW: Gastrointestinal tract (gut) health in the young pig. Pluske, JR. Animal Nutrition

Plant, soil, and water Microbiome

Deciphering the bacterial and fungal communities in clubroot-affected cabbage rhizosphere treated with Bacillus Subtilis XF-1. Liu, C. Agriculture, Ecosystems & Environment

REVIEW:Rhizospheric microorganisms as a solution for the recovery of soils contaminated by petroleum: A review. Janzen dos Santos, J. Journal of Environmental Management.

Food Microbiome

Different temperatures select distinctive acetic acid bacteria species and promotes organic acids production during Kombucha tea fermentation. De Filippis. Food Microbiology


REVIEW: Fluorescence activated cell-sorting principles and applications in microalgal biotechnology. Pereira, H. Algal Research

A-GAME: improving the assembly of pooled functional metagenomics sequence data. Chiara, M. BMC Genomics

Microbes in the News

Research Says Exercise Also Improves Your Gut Bacteria